Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0034982 mitochondrial protein processing	IBA GO_REF:0000033	ACCEPT	Summary: AFG3L2 directly processes mitochondrial substrates, including MRPL32 and multiple inner membrane proteins/carriers. Reason: Mitochondrial protein processing is a core biological role of the m-AAA protease alongside degradative quality control. Supporting Evidence: PMID:29932645 conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form PMID:41075794 SLC25A45-FLAG levels only increased in cells treated with siRNA targeting AFG3L2 PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
GO:0005745 m-AAA complex	IBA GO_REF:0000033	ACCEPT	Summary: AFG3L2 is a constituent of the mitochondrial m-AAA protease complex, as homohexamers and as heterohexamers with SPG7. Reason: The m-AAA complex is the correct cellular component context for AFG3L2 protease function. Supporting Evidence: PMID:31327635 The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7) PMID:14623864 paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane
GO:0004222 metalloendopeptidase activity	IBA GO_REF:0000033	ACCEPT	Summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit. Reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
GO:0004176 ATP-dependent peptidase activity	IEA GO_REF:0000002	ACCEPT	Summary: ATP-dependent peptidase activity accurately combines the ATPase and protease aspects of AFG3L2 function. Reason: The m-AAA protease uses ATP hydrolysis to unfold/translocate substrates and protease active sites to degrade them. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. PMID:19748354 we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes
GO:0004222 metalloendopeptidase activity	IEA GO_REF:0000002	ACCEPT	Summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit. Reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
GO:0005524 ATP binding	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: ATP binding is a true domain-associated property, but ATP hydrolysis is the informative catalytic annotation. Reason: Keep as a non-core molecular feature; core function should emphasize ATP hydrolysis and ATP-dependent peptidase activity. Supporting Evidence: PMID:19748354 we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes PMID:31327635 ATP-dependent translocation to unfold and degrade targeted proteins
GO:0005743 mitochondrial inner membrane	IEA GO_REF:0000120	ACCEPT	Summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side. Reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component. Supporting Evidence: PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0006508 proteolysis	IEA GO_REF:0000120	MODIFY	Summary: Generic proteolysis is correct but underspecified for the mitochondrial m-AAA protease role. Reason: The evidence supports mitochondrial substrate degradation and protein quality control, not merely generic proteolysis. Proposed replacements: mitochondrial protein catabolic process Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. file:projects/PROTEOSTASIS/reports/pn_projection/pn_projected_annotations.tsv This PN class groups mitochondrial protein-degradation pathways. GO mitochondrial protein catabolic process is the conservative shared target.
GO:0008270 zinc ion binding	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: Zinc binding is supported by the M41 metalloprotease active site but is not itself the core function. Reason: Keep as a cofactor/domain feature and emphasize metalloendopeptidase activity as the core molecular function. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
GO:0016020 membrane	IEA GO_REF:0000002	MODIFY	Summary: Membrane localization is correct but too broad. Reason: AFG3L2 is specifically an integral mitochondrial inner membrane protein. Proposed replacements: mitochondrial inner membrane Supporting Evidence: PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0016887 ATP hydrolysis activity	IEA GO_REF:0000120	ACCEPT	Summary: ATP hydrolysis is a core motor activity of the AAA+ ring that powers substrate unfolding and translocation. Reason: This is directly supported by m-AAA ATPase assays and AFG3L2 structural work tying ATP-dependent translocation to substrate degradation. Supporting Evidence: PMID:19748354 we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes PMID:31327635 ATP-dependent translocation to unfold and degrade targeted proteins
GO:0005515 protein binding	IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ...	MARK AS OVER ANNOTATED	Summary: The IPI row records binding to UniProtKB:P42858, but protein binding is too generic to describe AFG3L2 function. Reason: Specific interactions should be interpreted through m-AAA complex membership, substrate degradation, calcium regulation, or other informative process terms rather than the generic protein binding MF term. Supporting Evidence: PMID:32814053 Interactome maps are valuable resources to elucidate protein function and disease mechanisms.
GO:0005745 m-AAA complex	IEA GO_REF:0000120	ACCEPT	Summary: AFG3L2 is a constituent of the mitochondrial m-AAA protease complex, as homohexamers and as heterohexamers with SPG7. Reason: The m-AAA complex is the correct cellular component context for AFG3L2 protease function. Supporting Evidence: PMID:31327635 The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7) PMID:14623864 paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane
GO:0008237 metallopeptidase activity	IEA GO_REF:0000107	MODIFY	Summary: The annotation is directionally correct but too broad for AFG3L2. Reason: AFG3L2 is specifically supported as a metalloendopeptidase/m-AAA protease; use the more precise metalloendopeptidase activity term. Proposed replacements: metalloendopeptidase activity Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
GO:0016485 protein processing	IEA GO_REF:0000107	MODIFY	Summary: Protein processing is true but should be represented with the existing mitochondrial protein processing term. Reason: AFG3L2 processing events occur in mitochondria and are already captured more specifically by mitochondrial protein processing. Proposed replacements: mitochondrial protein processing Supporting Evidence: PMID:29932645 conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form PMID:41075794 SLC25A45-FLAG levels only increased in cells treated with siRNA targeting AFG3L2
GO:0016540 protein autoprocessing	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Autoprocessing of the imported precursor is described for AFG3L2, but it is ancillary to the mature protease role. Reason: Retain as non-core because the main biological function is degradation/processing of mitochondrial substrates. Supporting Evidence: file:human/AFG3L2/AFG3L2-uniprot.txt autocatalytic proteolytic processing to generate the proteolytically active mature form
GO:0051604 protein maturation	IEA GO_REF:0000120	MODIFY	Summary: Protein maturation is true for selected substrates but too generic. Reason: The evidence points to mitochondrial protein processing/maturation, especially MRPL32 and related mitochondrial substrates. Proposed replacements: mitochondrial protein processing Supporting Evidence: PMID:29932645 conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form PMID:41075794 SLC25A45-FLAG levels only increased in cells treated with siRNA targeting AFG3L2
GO:0110097 regulation of calcium import into the mitochondrion	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: AFG3L2 regulates mitochondrial calcium import by degrading unassembled EMRE before MCU complex assembly. Reason: This is a supported substrate-specific consequence of m-AAA proteolysis, but not the central gene-level function. Supporting Evidence: PMID:27642048 the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU PMID:28396416 mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis
GO:0005739 mitochondrion	IDA GO_REF:0000052	MODIFY	Summary: Mitochondrial localization is correct but less specific than the established inner-membrane localization. Reason: The earliest localization work supports mitochondria, and later biochemical/structural work resolves AFG3L2 to the mitochondrial inner membrane. Proposed replacements: mitochondrial inner membrane Supporting Evidence: PMID:10395799 Immunofluorescence studies revealed that AFG3L2 and paraplegin share a similar expression pattern and the same subcellular localization, the mitochondrial compartment. PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0004222 metalloendopeptidase activity	IMP PMID:41075794 SLC25A45 is required for mitochondrial uptake of methylated ...	ACCEPT	Summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit. Reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
GO:0034982 mitochondrial protein processing	IMP PMID:41075794 SLC25A45 is required for mitochondrial uptake of methylated ...	ACCEPT	Summary: AFG3L2 directly processes mitochondrial substrates, including MRPL32 and multiple inner membrane proteins/carriers. Reason: Mitochondrial protein processing is a core biological role of the m-AAA protease alongside degradative quality control. Supporting Evidence: PMID:29932645 conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form PMID:41075794 SLC25A45-FLAG levels only increased in cells treated with siRNA targeting AFG3L2 PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
GO:0005743 mitochondrial inner membrane	IDA PMID:31327635 Unique Structural Features of the Mitochondrial AAA+ Proteas...	ACCEPT	Summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side. Reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component. Supporting Evidence: PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0005745 m-AAA complex	IPI PMID:31327635 Unique Structural Features of the Mitochondrial AAA+ Proteas...	ACCEPT	Summary: AFG3L2 is a constituent of the mitochondrial m-AAA protease complex, as homohexamers and as heterohexamers with SPG7. Reason: The m-AAA complex is the correct cellular component context for AFG3L2 protease function. Supporting Evidence: PMID:31327635 The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7) PMID:14623864 paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane
GO:0034982 mitochondrial protein processing	IDA PMID:31327635 Unique Structural Features of the Mitochondrial AAA+ Proteas...	ACCEPT	Summary: AFG3L2 directly processes mitochondrial substrates, including MRPL32 and multiple inner membrane proteins/carriers. Reason: Mitochondrial protein processing is a core biological role of the m-AAA protease alongside degradative quality control. Supporting Evidence: PMID:29932645 conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form PMID:41075794 SLC25A45-FLAG levels only increased in cells treated with siRNA targeting AFG3L2 PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
GO:0005739 mitochondrion	HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an...	MODIFY	Summary: Mitochondrial localization is correct but less specific than the established inner-membrane localization. Reason: The earliest localization work supports mitochondria, and later biochemical/structural work resolves AFG3L2 to the mitochondrial inner membrane. Proposed replacements: mitochondrial inner membrane Supporting Evidence: PMID:10395799 Immunofluorescence studies revealed that AFG3L2 and paraplegin share a similar expression pattern and the same subcellular localization, the mitochondrial compartment. PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0141164 mitochondrial protein quality control	IDA PMID:26504172 Quality control of mitochondrial protein synthesis is requir...	ACCEPT	Summary: AFG3L2 performs mitochondrial protein quality control, especially for newly synthesized or misassembled inner-membrane proteins. Reason: This is a core process annotation supported by direct perturbation and mitochondrial translation/proteostasis studies. Supporting Evidence: PMID:26504172 The mitochondrial m-AAA protease subunit AFG3L2 is critical to this surveillance mechanism PMID:30683687 Responsive quality control mechanisms are needed to ensure that aberrant protein synthesis does not disrupt mitochondrial function. PMID:34718584 defects in the OXA1L-mediated insertion of MT-ATP6 nascent chains into the mitochondrial inner membrane are rapidly resolved by the AFG3L2 protease complex file:human/AFG3L2/AFG3L2-deep-research-falcon.md m-AAA proteases are IMM-embedded ATP-dependent protease complexes that provide protein quality control (PQC) by selective removal/processing of non-assembled or damaged mitochondrial proteins
GO:0141164 mitochondrial protein quality control	IDA PMID:30683687 Mitochondrial stress response triggered by defects in protei...	ACCEPT	Summary: AFG3L2 performs mitochondrial protein quality control, especially for newly synthesized or misassembled inner-membrane proteins. Reason: This is a core process annotation supported by direct perturbation and mitochondrial translation/proteostasis studies. Supporting Evidence: PMID:26504172 The mitochondrial m-AAA protease subunit AFG3L2 is critical to this surveillance mechanism PMID:30683687 Responsive quality control mechanisms are needed to ensure that aberrant protein synthesis does not disrupt mitochondrial function. PMID:34718584 defects in the OXA1L-mediated insertion of MT-ATP6 nascent chains into the mitochondrial inner membrane are rapidly resolved by the AFG3L2 protease complex
GO:0141164 mitochondrial protein quality control	IDA PMID:34718584 Translation of MT-ATP6 pathogenic variants reveals distinct ...	ACCEPT	Summary: AFG3L2 performs mitochondrial protein quality control, especially for newly synthesized or misassembled inner-membrane proteins. Reason: This is a core process annotation supported by direct perturbation and mitochondrial translation/proteostasis studies. Supporting Evidence: PMID:26504172 The mitochondrial m-AAA protease subunit AFG3L2 is critical to this surveillance mechanism PMID:30683687 Responsive quality control mechanisms are needed to ensure that aberrant protein synthesis does not disrupt mitochondrial function. PMID:34718584 defects in the OXA1L-mediated insertion of MT-ATP6 nascent chains into the mitochondrial inner membrane are rapidly resolved by the AFG3L2 protease complex
GO:0004222 metalloendopeptidase activity	IDA PMID:29545505 m-AAA and i-AAA complexes coordinate to regulate OMA1, the s...	ACCEPT	Summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit. Reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
GO:0004222 metalloendopeptidase activity	IDA PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ...	ACCEPT	Summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit. Reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
GO:0004222 metalloendopeptidase activity	IDA PMID:28396416 Proteolytic control of the mitochondrial calcium uniporter c...	ACCEPT	Summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit. Reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
GO:0005743 mitochondrial inner membrane	IDA PMID:37917749 Autoregulatory control of mitochondrial glutathione homeosta...	ACCEPT	Summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side. Reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component. Supporting Evidence: PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0005745 m-AAA complex	IDA PMID:28396416 Proteolytic control of the mitochondrial calcium uniporter c...	ACCEPT	Summary: AFG3L2 is a constituent of the mitochondrial m-AAA protease complex, as homohexamers and as heterohexamers with SPG7. Reason: The m-AAA complex is the correct cellular component context for AFG3L2 protease function. Supporting Evidence: PMID:31327635 The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7) PMID:14623864 paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane
GO:0110097 regulation of calcium import into the mitochondrion	IDA PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ...	KEEP AS NON CORE	Summary: AFG3L2 regulates mitochondrial calcium import by degrading unassembled EMRE before MCU complex assembly. Reason: This is a supported substrate-specific consequence of m-AAA proteolysis, but not the central gene-level function. Supporting Evidence: PMID:27642048 the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU PMID:28396416 mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis
GO:0110097 regulation of calcium import into the mitochondrion	IDA PMID:28396416 Proteolytic control of the mitochondrial calcium uniporter c...	KEEP AS NON CORE	Summary: AFG3L2 regulates mitochondrial calcium import by degrading unassembled EMRE before MCU complex assembly. Reason: This is a supported substrate-specific consequence of m-AAA proteolysis, but not the central gene-level function. Supporting Evidence: PMID:27642048 the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU PMID:28396416 mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis
GO:0004222 metalloendopeptidase activity	IDA PMID:37917749 Autoregulatory control of mitochondrial glutathione homeosta...	ACCEPT	Summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit. Reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
GO:0004222 metalloendopeptidase activity	IDA PMID:38157846 Dual regulation of SLC25A39 by AFG3L2 and iron controls mito...	ACCEPT	Summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit. Reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
GO:0005743 mitochondrial inner membrane	TAS PMID:31327635 Unique Structural Features of the Mitochondrial AAA+ Proteas...	ACCEPT	Summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side. Reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component. Supporting Evidence: PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0030163 protein catabolic process	IDA PMID:37917749 Autoregulatory control of mitochondrial glutathione homeosta...	MODIFY	Summary: Protein catabolic process is correct but too broad for the directly supported mitochondrial degradation role. Reason: AFG3L2 degrades mitochondrial inner membrane and matrix-facing substrates; the PN projection to mitochondrial protein catabolic process is conservative and literature-supported. Proposed replacements: mitochondrial protein catabolic process Supporting Evidence: PMID:37917749 Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2. PMID:38157846 mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1 file:projects/PROTEOSTASIS/reports/pn_projection/pn_projected_annotations.tsv This PN class groups mitochondrial protein-degradation pathways. GO mitochondrial protein catabolic process is the conservative shared target.
GO:0030163 protein catabolic process	IDA PMID:38157846 Dual regulation of SLC25A39 by AFG3L2 and iron controls mito...	MODIFY	Summary: Protein catabolic process is correct but too broad for the directly supported mitochondrial degradation role. Reason: AFG3L2 degrades mitochondrial inner membrane and matrix-facing substrates; the PN projection to mitochondrial protein catabolic process is conservative and literature-supported. Proposed replacements: mitochondrial protein catabolic process Supporting Evidence: PMID:37917749 Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2. PMID:38157846 mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1 file:projects/PROTEOSTASIS/reports/pn_projection/pn_projected_annotations.tsv This PN class groups mitochondrial protein-degradation pathways. GO mitochondrial protein catabolic process is the conservative shared target.
GO:0072753 cellular response to glutathione	IDA PMID:37917749 Autoregulatory control of mitochondrial glutathione homeosta...	KEEP AS NON CORE	Summary: AFG3L2 participates in the glutathione-response circuit by degrading SLC25A39 when mitochondrial glutathione is sufficient. Reason: The annotation reflects a specific regulatory substrate and metabolite-feedback axis, but the core function remains mitochondrial proteolysis. Supporting Evidence: PMID:37917749 Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2. PMID:38157846 mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1
GO:0072753 cellular response to glutathione	IDA PMID:38157846 Dual regulation of SLC25A39 by AFG3L2 and iron controls mito...	KEEP AS NON CORE	Summary: AFG3L2 participates in the glutathione-response circuit by degrading SLC25A39 when mitochondrial glutathione is sufficient. Reason: The annotation reflects a specific regulatory substrate and metabolite-feedback axis, but the core function remains mitochondrial proteolysis. Supporting Evidence: PMID:37917749 Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2. PMID:38157846 mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1
GO:0004222 metalloendopeptidase activity	IDA PMID:19748354 An intersubunit signaling network coordinates ATP hydrolysis...	ACCEPT	Summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit. Reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
GO:0004222 metalloendopeptidase activity	IDA PMID:29932645 Dissecting Substrate Specificities of the Mitochondrial AFG3...	ACCEPT	Summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit. Reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
GO:0004222 metalloendopeptidase activity	IDA PMID:31327635 Unique Structural Features of the Mitochondrial AAA+ Proteas...	ACCEPT	Summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit. Reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
GO:0005745 m-AAA complex	IDA PMID:19748354 An intersubunit signaling network coordinates ATP hydrolysis...	ACCEPT	Summary: AFG3L2 is a constituent of the mitochondrial m-AAA protease complex, as homohexamers and as heterohexamers with SPG7. Reason: The m-AAA complex is the correct cellular component context for AFG3L2 protease function. Supporting Evidence: PMID:31327635 The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7) PMID:14623864 paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane
GO:0005745 m-AAA complex	IDA PMID:31327635 Unique Structural Features of the Mitochondrial AAA+ Proteas...	ACCEPT	Summary: AFG3L2 is a constituent of the mitochondrial m-AAA protease complex, as homohexamers and as heterohexamers with SPG7. Reason: The m-AAA complex is the correct cellular component context for AFG3L2 protease function. Supporting Evidence: PMID:31327635 The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7) PMID:14623864 paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane
GO:0016887 ATP hydrolysis activity	IDA PMID:19748354 An intersubunit signaling network coordinates ATP hydrolysis...	ACCEPT	Summary: ATP hydrolysis is a core motor activity of the AAA+ ring that powers substrate unfolding and translocation. Reason: This is directly supported by m-AAA ATPase assays and AFG3L2 structural work tying ATP-dependent translocation to substrate degradation. Supporting Evidence: PMID:19748354 we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes PMID:31327635 ATP-dependent translocation to unfold and degrade targeted proteins
GO:0016887 ATP hydrolysis activity	IDA PMID:31327635 Unique Structural Features of the Mitochondrial AAA+ Proteas...	ACCEPT	Summary: ATP hydrolysis is a core motor activity of the AAA+ ring that powers substrate unfolding and translocation. Reason: This is directly supported by m-AAA ATPase assays and AFG3L2 structural work tying ATP-dependent translocation to substrate degradation. Supporting Evidence: PMID:19748354 we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes PMID:31327635 ATP-dependent translocation to unfold and degrade targeted proteins
GO:0051604 protein maturation	IDA PMID:29932645 Dissecting Substrate Specificities of the Mitochondrial AFG3...	MODIFY	Summary: Protein maturation is true for selected substrates but too generic. Reason: The evidence points to mitochondrial protein processing/maturation, especially MRPL32 and related mitochondrial substrates. Proposed replacements: mitochondrial protein processing Supporting Evidence: PMID:29932645 conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form PMID:41075794 SLC25A45-FLAG levels only increased in cells treated with siRNA targeting AFG3L2
GO:0005515 protein binding	IPI PMID:35912435 Regulation of mitochondrial proteostasis by the proton gradi...	MARK AS OVER ANNOTATED	Summary: The IPI row records binding to UniProtKB:Q9H3K2, but protein binding is too generic to describe AFG3L2 function. Reason: Specific interactions should be interpreted through m-AAA complex membership, substrate degradation, calcium regulation, or other informative process terms rather than the generic protein binding MF term. Supporting Evidence: PMID:35912435 Besides these expected interactors, TMBIM5 (also known as GHITM or MICS1) was highly enriched in AFG3L2 precipitates
GO:0006508 proteolysis	IDA PMID:35912435 Regulation of mitochondrial proteostasis by the proton gradi...	MODIFY	Summary: Generic proteolysis is correct but underspecified for the mitochondrial m-AAA protease role. Reason: The evidence supports mitochondrial substrate degradation and protein quality control, not merely generic proteolysis. Proposed replacements: mitochondrial protein catabolic process Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. file:projects/PROTEOSTASIS/reports/pn_projection/pn_projected_annotations.tsv This PN class groups mitochondrial protein-degradation pathways. GO mitochondrial protein catabolic process is the conservative shared target.
GO:0004222 metalloendopeptidase activity	IDA PMID:22354088 Mitochondrial processing peptidase regulates PINK1 processin...	ACCEPT	Summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit. Reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
GO:0005739 mitochondrion	IDA PMID:22354088 Mitochondrial processing peptidase regulates PINK1 processin...	MODIFY	Summary: Mitochondrial localization is correct but less specific than the established inner-membrane localization. Reason: The earliest localization work supports mitochondria, and later biochemical/structural work resolves AFG3L2 to the mitochondrial inner membrane. Proposed replacements: mitochondrial inner membrane Supporting Evidence: PMID:10395799 Immunofluorescence studies revealed that AFG3L2 and paraplegin share a similar expression pattern and the same subcellular localization, the mitochondrial compartment. PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0033619 membrane protein proteolysis	IDA PMID:22354088 Mitochondrial processing peptidase regulates PINK1 processin...	ACCEPT	Summary: AFG3L2 participates in proteolysis of mitochondrial membrane-associated proteins such as PINK1 and inner-membrane substrates. Reason: The term is consistent with direct m-AAA substrate degradation, although the added mitochondrial protein catabolic process term captures the broader mitochondrial context. Supporting Evidence: PMID:22354088 we identified four mitochondrial proteases, mitochondrial processing peptidase (MPP), presenilin-associated rhomboid-like protease (PARL), m-AAA and ClpXP, involved in PINK1 degradation PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
GO:0005515 protein binding	IPI PMID:26387735 SPG7 Is an Essential and Conserved Component of the Mitochon...	MARK AS OVER ANNOTATED	Summary: The IPI row records binding to UniProtKB:Q9UQ90, but protein binding is too generic to describe AFG3L2 function. Reason: Specific interactions should be interpreted through m-AAA complex membership, substrate degradation, calcium regulation, or other informative process terms rather than the generic protein binding MF term. Supporting Evidence: PMID:14623864 To explore a potential physical interaction between paraplegin and AFG3L2, we performed coimmunoprecipitation studies in HEK293. PMID:26387735 HA antibody immunoprecipitated a known SPG7 binding partner AFG3L2
GO:0005743 mitochondrial inner membrane	ISS GO_REF:0000024	ACCEPT	Summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side. Reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component. Supporting Evidence: PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0016485 protein processing	ISS GO_REF:0000024	MODIFY	Summary: Protein processing is true but should be represented with the existing mitochondrial protein processing term. Reason: AFG3L2 processing events occur in mitochondria and are already captured more specifically by mitochondrial protein processing. Proposed replacements: mitochondrial protein processing Supporting Evidence: PMID:29932645 conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form PMID:41075794 SLC25A45-FLAG levels only increased in cells treated with siRNA targeting AFG3L2
GO:0016540 protein autoprocessing	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: Autoprocessing of the imported precursor is described for AFG3L2, but it is ancillary to the mature protease role. Reason: Retain as non-core because the main biological function is degradation/processing of mitochondrial substrates. Supporting Evidence: file:human/AFG3L2/AFG3L2-uniprot.txt autocatalytic proteolytic processing to generate the proteolytically active mature form
GO:0005743 mitochondrial inner membrane	TAS Reactome:R-HSA-8949649	ACCEPT	Summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side. Reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component. Supporting Evidence: PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0005743 mitochondrial inner membrane	TAS Reactome:R-HSA-8949659	ACCEPT	Summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side. Reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component. Supporting Evidence: PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0005743 mitochondrial inner membrane	TAS Reactome:R-HSA-8949661	ACCEPT	Summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side. Reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component. Supporting Evidence: PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0005743 mitochondrial inner membrane	TAS Reactome:R-HSA-9838627	ACCEPT	Summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side. Reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component. Supporting Evidence: PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0005743 mitochondrial inner membrane	TAS Reactome:R-HSA-9839053	ACCEPT	Summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side. Reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component. Supporting Evidence: PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0005743 mitochondrial inner membrane	TAS Reactome:R-HSA-9839059	ACCEPT	Summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side. Reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component. Supporting Evidence: PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0005743 mitochondrial inner membrane	TAS Reactome:R-HSA-9839105	ACCEPT	Summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side. Reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component. Supporting Evidence: PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0005743 mitochondrial inner membrane	TAS Reactome:R-HSA-9839113	ACCEPT	Summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side. Reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component. Supporting Evidence: PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0005743 mitochondrial inner membrane	TAS Reactome:R-HSA-9839149	ACCEPT	Summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side. Reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component. Supporting Evidence: PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0005515 protein binding	IPI PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ...	MARK AS OVER ANNOTATED	Summary: The IPI row records binding to UniProtKB:Q8WWC4, but protein binding is too generic to describe AFG3L2 function. Reason: Specific interactions should be interpreted through m-AAA complex membership, substrate degradation, calcium regulation, or other informative process terms rather than the generic protein binding MF term. Supporting Evidence: PMID:27642048 MAIP1 assists biogenesis of the MCU subunit EMRE, the m-AAA protease degrades non-assembled EMRE PMID:27642048 the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU
GO:0005515 protein binding	IPI PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ...	MARK AS OVER ANNOTATED	Summary: The IPI row records binding to UniProtKB:Q9H4I9, but protein binding is too generic to describe AFG3L2 function. Reason: Specific interactions should be interpreted through m-AAA complex membership, substrate degradation, calcium regulation, or other informative process terms rather than the generic protein binding MF term. Supporting Evidence: PMID:27642048 MAIP1 assists biogenesis of the MCU subunit EMRE, the m-AAA protease degrades non-assembled EMRE PMID:27642048 the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU
GO:0006508 proteolysis	IMP PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ...	MODIFY	Summary: Generic proteolysis is correct but underspecified for the mitochondrial m-AAA protease role. Reason: The evidence supports mitochondrial substrate degradation and protein quality control, not merely generic proteolysis. Proposed replacements: mitochondrial protein catabolic process Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. file:projects/PROTEOSTASIS/reports/pn_projection/pn_projected_annotations.tsv This PN class groups mitochondrial protein-degradation pathways. GO mitochondrial protein catabolic process is the conservative shared target.
GO:0007409 axonogenesis	IMP PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ...	KEEP AS NON CORE	Summary: Axonogenesis reflects a neuronal phenotype of impaired m-AAA protease function rather than a direct molecular role. Reason: Retain as non-core/developmental consequence; do not use it to define AFG3L2 core function. Supporting Evidence: PMID:31327635 m-AAA proteases are essential for axonal development in mammals PMID:27642048 Loss of the m-AAA protease results in accumulation of constitutively active MCU-EMRE channels
GO:0008237 metallopeptidase activity	IMP PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ...	MODIFY	Summary: The annotation is directionally correct but too broad for AFG3L2. Reason: AFG3L2 is specifically supported as a metalloendopeptidase/m-AAA protease; use the more precise metalloendopeptidase activity term. Proposed replacements: metalloendopeptidase activity Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
GO:0036444 calcium import into the mitochondrion	IMP PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ...	MODIFY	Summary: The calcium-import phenotype is mediated through regulation of EMRE/MCU assembly rather than direct calcium transport by AFG3L2. Reason: Use regulation of calcium import into the mitochondrion rather than annotating AFG3L2 as directly involved in calcium import. Proposed replacements: regulation of calcium import into the mitochondrion Supporting Evidence: PMID:27642048 the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU PMID:28396416 mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis
GO:0051560 mitochondrial calcium ion homeostasis	IMP PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ...	KEEP AS NON CORE	Summary: AFG3L2 contributes to mitochondrial calcium homeostasis through EMRE turnover and MCU gatekeeper assembly. Reason: Supported but downstream/substrate-specific relative to the m-AAA protease quality-control function. Supporting Evidence: PMID:27642048 the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU PMID:28396416 mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis
GO:0005515 protein binding	IPI PMID:14623864 Loss of m-AAA protease in mitochondria causes complex I defi...	MARK AS OVER ANNOTATED	Summary: The IPI row records binding to UniProtKB:Q9UQ90, but protein binding is too generic to describe AFG3L2 function. Reason: Specific interactions should be interpreted through m-AAA complex membership, substrate degradation, calcium regulation, or other informative process terms rather than the generic protein binding MF term. Supporting Evidence: PMID:14623864 To explore a potential physical interaction between paraplegin and AFG3L2, we performed coimmunoprecipitation studies in HEK293. PMID:26387735 HA antibody immunoprecipitated a known SPG7 binding partner AFG3L2
GO:0005739 mitochondrion	TAS PMID:10395799 Identification and characterization of AFG3L2, a novel parap...	MODIFY	Summary: Mitochondrial localization is correct but less specific than the established inner-membrane localization. Reason: The earliest localization work supports mitochondria, and later biochemical/structural work resolves AFG3L2 to the mitochondrial inner membrane. Proposed replacements: mitochondrial inner membrane Supporting Evidence: PMID:10395799 Immunofluorescence studies revealed that AFG3L2 and paraplegin share a similar expression pattern and the same subcellular localization, the mitochondrial compartment. PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
GO:0035694 mitochondrial protein catabolic process	IC PMID:31327635 Unique Structural Features of the Mitochondrial AAA+ Proteas...	NEW	Summary: Proposed new annotation from the Proteostasis Network projection. AFG3L2 directly degrades mitochondrial substrates as an inner-membrane m-AAA protease, so mitochondrial protein catabolic process is a conservative addition. Reason: The PN projection flagged GO:0035694 as more specific than the existing generic protein catabolic process annotation. Literature supports mitochondrial substrate degradation, while the parallel PN matrix localization projection is not accepted because AFG3L2 is an inner membrane protein with matrix-facing catalytic domains. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. PMID:37917749 Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2. file:projects/PROTEOSTASIS/reports/pn_projection/pn_projected_annotations.tsv This PN class groups mitochondrial protein-degradation pathways. GO mitochondrial protein catabolic process is the conservative shared target. file:human/AFG3L2/AFG3L2-deep-research-falcon.md m-AAA proteases are IMM-embedded ATP-dependent protease complexes that provide protein quality control (PQC) by selective removal/processing of non-assembled or damaged mitochondrial proteins

Core Functions

ATP-dependent zinc metalloendopeptidase activity in the mitochondrial m-AAA protease. AFG3L2 uses its AAA+ motor to engage and unfold mitochondrial substrates and its M41 protease active sites to cleave them, supporting mitochondrial protein catabolic process, mitochondrial protein processing, and mitochondrial protein quality control.

Molecular Function:

metalloendopeptidase activity

Directly Involved In:

mitochondrial protein catabolic process mitochondrial protein processing mitochondrial protein quality control

Cellular Locations:

mitochondrial inner membrane

In Complex:

m-AAA complex

Supporting Evidence:

PMID:31327635
structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
PMID:29932645
Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
PMID:26504172
The mitochondrial m-AAA protease subunit AFG3L2 is critical to this surveillance mechanism
PMID:29932645
conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form

AAA+ ATP hydrolysis that powers substrate unfolding, membrane-proximal engagement, and translocation into the proteolytic chamber of the m-AAA complex.

Molecular Function:

ATP hydrolysis activity

Directly Involved In:

mitochondrial protein catabolic process

Cellular Locations:

mitochondrial inner membrane

In Complex:

m-AAA complex

Supporting Evidence:

PMID:19748354
we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes
PMID:31327635
ATP-dependent translocation to unfold and degrade targeted proteins

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000024

Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000052

Gene Ontology annotation based on curation of immunofluorescence data

GO_REF:0000107

Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:10395799

Identification and characterization of AFG3L2, a novel paraplegin-related gene.

PMID:14623864

Loss of m-AAA protease in mitochondria causes complex I deficiency and increased sensitivity to oxidative stress in hereditary spastic paraplegia.

PMID:19748354

An intersubunit signaling network coordinates ATP hydrolysis by m-AAA proteases.

PMID:22354088

Mitochondrial processing peptidase regulates PINK1 processing, import and Parkin recruitment.

PMID:26387735

SPG7 Is an Essential and Conserved Component of the Mitochondrial Permeability Transition Pore.

PMID:26504172

Quality control of mitochondrial protein synthesis is required for membrane integrity and cell fitness.

PMID:27642048

The m-AAA Protease Associated with Neurodegeneration Limits MCU Activity in Mitochondria.

PMID:28396416

Proteolytic control of the mitochondrial calcium uniporter complex.

PMID:29545505

m-AAA and i-AAA complexes coordinate to regulate OMA1, the stress-activated supervisor of mitochondrial dynamics.

PMID:29932645

Dissecting Substrate Specificities of the Mitochondrial AFG3L2 Protease.

PMID:30683687

Mitochondrial stress response triggered by defects in protein synthesis quality control.

PMID:31327635

Unique Structural Features of the Mitochondrial AAA+ Protease AFG3L2 Reveal the Molecular Basis for Activity in Health and Disease.

PMID:32814053

Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.

PMID:34718584

Translation of MT-ATP6 pathogenic variants reveals distinct regulatory consequences from the co-translational quality control of mitochondrial protein synthesis.

PMID:34800366

Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context.

PMID:35912435

Regulation of mitochondrial proteostasis by the proton gradient.

PMID:37917749

Autoregulatory control of mitochondrial glutathione homeostasis.

PMID:38157846

Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis.

PMID:41075794

SLC25A45 is required for mitochondrial uptake of methylated amino acids and de novo carnitine biosynthesis.

Reactome:R-HSA-8949649

PMPCA:PMPCB cleaves the transit peptide of proSMDT1 (proEMRE)

Reactome:R-HSA-8949659

AFG3L2 (m-AAA protease) degrades SMDT1 that is not assembled in MCU

Reactome:R-HSA-8949661

C2orf47:AFG3L2 binds the transit peptide of SMDT1

Reactome:R-HSA-9838627

AFG3L2 binds mitochondrial inner membrane proteins

Reactome:R-HSA-9839053

AFG3L2:SPG7 binds SMDT1 (EMRE)

Reactome:R-HSA-9839059

AFG3L2:SPG7 degrades SMDT1 (EMRE)

Reactome:R-HSA-9839105

AFG3L2 degrades mitochondrial matrix proteins

Reactome:R-HSA-9839113

AFG3L2 degrades mitochondrial inner membrane proteins

Reactome:R-HSA-9839149

AFG3L2 binds mitochondrial matrix proteins

file:human/AFG3L2/AFG3L2-uniprot.txt

UniProtKB record for human AFG3L2 (Q9Y4W6)

file:human/AFG3L2/AFG3L2-deep-research-falcon.md

Falcon deep research report for human AFG3L2

file:human/AFG3L2/AFG3L2-notes.md

AFG3L2 curator notes for Proteostasis PN review

file:projects/PROTEOSTASIS/reports/pn_projection/pn_projected_annotations.tsv

Proteostasis Network projected GO annotations report

file:projects/PROTEOSTASIS/mappings/mitochondrial_proteostasis.yaml

Proteostasis Network mitochondrial proteostasis mapping

Suggested Experiments

Experiment: Combine pulse-chase proteomics in AFG3L2 knockout/rescue cells with degron-mutant substrate panels for SLC25A39, SLC25A45, EMRE, and TMBIM5, measuring substrate half-life, AFG3L2 association, and mitochondrial metabolite or calcium readouts.

Hypothesis: AFG3L2 substrates can be prioritized by matrix-exposed degrons and metabolite-sensitive conformational states rather than by generic inner-membrane localization alone.

Type: proteomics and targeted substrate-turnover assays

Deep Research

Falcon

(AFG3L2-deep-research-falcon.md)

Comprehensive Research Report: Human **AFG3L2** (UniProt **Q9Y4W6**) — Functional Annotation and Disease Relevance Falcon Edison Scientific Literature 25 citations 1 artifacts 2026-06-03T09:50:59.432835

Edison artifact artifact-00 (text/markdown)

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Comprehensive Research Report: Human AFG3L2 (UniProt Q9Y4W6) — Functional Annotation and Disease Relevance

Executive summary

AFG3L2 (UniProt Q9Y4W6) encodes a mitochondrial inner membrane (IMM) m-AAA protease subunit that assembles as homo-hexamers or hetero-hexamers with SPG7/paraplegin. The complex performs ATP-dependent, zinc-metalloprotease proteolysis (protein quality control and regulatory processing) with catalytic sites facing the mitochondrial matrix. Recent 2023–2024 literature substantially expanded the experimentally supported substrate set (e.g., SLC25A39 for glutathione homeostasis; MRPL32/bL32m for mitoribosome assembly; EMRE for mitochondrial Ca2+ regulation) and connected AFG3L2 activity to cell-state regulation, including hypoxia signaling via HIF1α–mTORC1 and stress signaling via OMA1–DELE1–HRI integrated stress response (ISR). Pathogenic variants cause a spectrum from dominant SCA28 and dominant optic atrophy 12 (DOA12/OPA12) to recessive early-onset SPAX5, with emerging preclinical therapeutic strategies centered on ISR tuning (e.g., Sephin-1) in SPAX5 models. (franchino2024sustainedoma1mediatedintegrated pages 1-2, dastidar2024multifacetedrolesof pages 1-2, liu2023autoregulatorycontrolof pages 3-4, chandragiri2024afg3l2mediatedproteolysisrestricts pages 9-13)

1) Gene/protein identity verification (mandatory)

The gene symbol AFG3L2 in the recent literature matches the UniProt-defined target Q9Y4W6: a mitochondrial inner membrane m-AAA protease component with AAA+ ATPase and zinc metalloprotease activities, assembling into m-AAA protease complexes (homo-oligomeric AFG3L2 or hetero-oligomeric AFG3L2–SPG7). These defining characteristics are repeatedly stated in 2023–2024 review and primary sources. (franchino2024sustainedoma1mediatedintegrated pages 1-2, dastidar2024multifacetedrolesof pages 1-2, dastidar2024multifacetedrolesof pages 2-5, khalimonchuk2023moleculardeterminantsof pages 6-8)

2) Key concepts and definitions (current understanding)

2.1 m-AAA protease and mitochondrial proteostasis

m-AAA proteases are IMM-embedded ATP-dependent protease complexes that provide protein quality control (PQC) by selective removal/processing of non-assembled or damaged mitochondrial proteins, thereby supporting inner membrane integrity and organelle function. AFG3L2-containing m-AAA is explicitly described as a core component of IMM quality control mediating selective degradation. (franchino2024sustainedoma1mediatedintegrated pages 1-2)

2.2 Domain logic and catalytic mechanism (AAA+ ATPase + Zn metalloprotease)

AFG3L2 is functionally defined by:
- an AAA+ ATPase module that uses ATP hydrolysis to engage, unfold, and translocate substrates through the central pore of the hexamer; and
- a C-terminal zinc metalloprotease domain that cleaves substrates after translocation.

A 2024 review describes ATP-stabilized hexamer assembly and a mechanistic sequence: substrate recruitment, ATP-dependent pore-loop engagement/translocation, followed by cleavage at a Zn-associated protease site. (dastidar2024multifacetedrolesof pages 1-2, dastidar2024multifacetedrolesof pages 2-5)

2.3 Subcellular localization and topology

AFG3L2 localizes to the mitochondrial inner membrane with catalytic faces oriented to the matrix (matrix-facing AAA+ and proteolytic sites). (franchino2024sustainedoma1mediatedintegrated pages 1-2, khalimonchuk2023moleculardeterminantsof pages 6-8, chandragiri2024afg3l2mediatedproteolysisrestricts pages 1-5)

3) Primary molecular function: reaction, substrate specificity, and pathways

3.1 Primary biochemical function

AFG3L2’s primary function is ATP-dependent proteolysis (metalloprotease EC 3.4.24.- class in UniProt terms) of specific mitochondrial substrates and misfolded/damaged IMM-associated proteins, coupled to ATP-dependent unfolding/translocation by its AAA+ motor. This is not a passive “housekeeping” role: multiple studies support regulatory substrate processing/degradation that tunes mitochondrial metabolism, Ca2+ transport, and gene expression. (franchino2024sustainedoma1mediatedintegrated pages 1-2, dastidar2024multifacetedrolesof pages 2-5, chandragiri2024afg3l2mediatedproteolysisrestricts pages 1-5)

3.2 Experimentally supported substrates (high-confidence examples)

3.2.1 SLC25A39 (mitochondrial glutathione transporter) — metabolic feedback control (2023)

A 2023 Science paper establishes a direct functional axis in which AFG3L2 degrades SLC25A39 under physiological conditions. Key quantitative data:
- SLC25A39 has an estimated half-life of ~15 minutes at baseline.
- Mitochondrial glutathione (GSH) depletion stabilizes SLC25A39 to >300 minutes.
- Glutathione supplementation restores rapid degradation.
A CRISPR screen of mitochondrial peptidases identified AFG3L2 as the only significant hit controlling this regulation, supporting substrate specificity and a compartmentalized feedback loop for mitochondrial GSH homeostasis. (liu2023autoregulatorycontrolof pages 3-4)

3.2.2 MRPL32 / bL32m (mitoribosome biogenesis)

Recent sources describe m-AAA/AFG3L2 as supporting mitochondrial ribosome assembly via processing/biogenesis of the ribosomal subunit bL32m (MRPL32). (chandragiri2024afg3l2mediatedproteolysisrestricts pages 1-5, khalimonchuk2023moleculardeterminantsof pages 6-8)

3.2.3 EMRE (MCU regulator) — mitochondrial Ca2+ handling

AFG3L2/m-AAA is connected to maturation/turnover of EMRE, a regulatory component of the mitochondrial calcium uniporter. This links AFG3L2 proteolysis to mitochondrial Ca2+ uptake control. (chandragiri2024afg3l2mediatedproteolysisrestricts pages 1-5, khalimonchuk2023moleculardeterminantsof pages 6-8)

3.2.4 TIMMDC1 (Complex I assembly factor)

A 2024 preprint reports TIMMDC1 as an AFG3L2 substrate whose degradation links AFG3L2 to complex I assembly control and OXPHOS remodeling. (chandragiri2024afg3l2mediatedproteolysisrestricts pages 1-5, chandragiri2024afg3l2mediatedproteolysisrestricts pages 5-9)

3.2.5 TMBIM5/GHITM (Ca2+/H+ homeostasis; inhibitor-substrate duality)

In hypoxia-linked remodeling, TMBIM5 (GHITM) is described as both a substrate and an inhibitor/modulator of AFG3L2, implying feedback regulation that connects protease activity to mitochondrial ion homeostasis. (chandragiri2024afg3l2mediatedproteolysisrestricts pages 13-16)

3.2.6 Expanded substrate landscape in hypoxia: RNA metabolism and biogenesis factors (2024)

Proteomic evidence under hypoxia suggests AFG3L2 targets numerous factors involved in mitochondrial gene expression and RNA granules, including LRPPRC, SLIRP, MTPAP, POLRMT, TFB2M, DHX30, GRSF1, as well as import factors (PAM16, DNAJC15, TIMM17A). These data support a model where AFG3L2 proteolysis can restrict mitochondrial biogenesis and gene expression under defined signaling conditions rather than only clearing misfolded proteins. (chandragiri2024afg3l2mediatedproteolysisrestricts pages 13-16)

4) Recent developments and latest research (prioritize 2023–2024)

4.1 2023: AFG3L2 couples glutathione availability to transporter turnover

The Liu et al. (Science, Nov 2023) study is a major mechanistic advance: it defines a concrete, quantitative, metabolite-coupled protease–transporter feedback loop in mitochondria, where GSH levels gate AFG3L2-mediated degradation of SLC25A39. This provides a molecular explanation for how mitochondria can regulate a key metabolite transporter post-translationally. Publication date: Nov 2023. URL: https://doi.org/10.1126/science.adf4154 (liu2023autoregulatorycontrolof pages 3-4)

4.2 2024: Disease mechanism and therapy concept in SPAX5 — ISR as protective output

Franchino et al. (Brain, Oct 2024) connect AFG3L2 deficiency to:
- accumulation of mitochondria-encoded proteins and mitochondrial proteotoxicity,
- OMA1 overactivation with OPA1 over-processing and mitochondrial fragmentation, and
- activation of the OMA1–DELE1–HRI ISR (elevated eIF2α phosphorylation; increased ATF4; upregulation of targets including Chop, Chac1, Ppp1r15a, Fgf21).

Importantly, they show pharmacologic potentiation of ISR via Sephin-1 improves growth of SPAX5 fibroblasts, improves Purkinje neuron survival/arborization ex vivo, and extends lifespan and improves cerebellar/mitochondrial phenotypes in Afg3l2−/− mice—supporting ISR modulation as a plausible therapeutic direction. Publication date: Oct 2024. URL: https://doi.org/10.1093/brain/awad340 (franchino2024sustainedoma1mediatedintegrated pages 1-2)

4.3 2024: Hypoxia signaling connects AFG3L2 to control of mitochondrial biogenesis and gene expression

A 2024 preprint reports that AFG3L2 proteolysis is activated in hypoxia along a HIF1α–mTORC1 axis; regulation is primarily post-translational (activity changes without requiring increased AFG3L2 abundance). Quantitative scope: proteomics suggests dozens of candidate substrates, including 38 proteins reduced with amino-acid starvation and 72 proteins decreased in hypoxia in an AFG3L2-dependent manner. (chandragiri2024afg3l2mediatedproteolysisrestricts pages 9-13)

This work further positions AFG3L2 as a regulated node in mitochondrial remodeling rather than a purely constitutive PQC enzyme. Publication date: Sep 2024 (bioRxiv). URL: https://doi.org/10.1101/2024.09.27.615438 (chandragiri2024afg3l2mediatedproteolysisrestricts pages 9-13)

5) Current applications and real-world implementations

5.1 Clinical genetics and diagnostics

AFG3L2 is implemented clinically primarily through molecular genetic testing for hereditary ataxia and optic neuropathy. A 2024 diagnostic classification review notes that for SCA28, >99% of reported cases are due to SNVs or small intragenic deletions/insertions (with copy-number changes reported as extremely rare), guiding practical test selection (sequencing prioritized; CNV assessment secondary). (lopergolo2024autosomalrecessivecerebellar pages 4-5)

Reviews emphasize that multigene panels and/or clinical exome sequencing support diagnosis, particularly when common ataxia causes are excluded. (dastidar2024multifacetedrolesof pages 15-16, dastidar2024multifacetedrolesof pages 10-11)

5.2 Preclinical therapeutic strategies with translational logic

ISR tuning as therapy (SPAX5): Sephin-1 improved multiple cellular and organismal endpoints in Afg3l2 deficiency models, providing a concrete lead for future translational development and defining potential pharmacodynamic biomarkers (eIF2α phosphorylation; ATF4 targets). (franchino2024sustainedoma1mediatedintegrated pages 1-2)
Supportive care remains standard for SCA28: reviews indicate no disease-modifying therapy currently; management is supportive and rehabilitative. (dastidar2024multifacetedrolesof pages 15-16)

5.3 Biomarkers and mechanistic readouts

A 2024 Brain study provides a coherent biomarker axis in patient fibroblasts and mouse cerebellum: increased eIF2α phosphorylation, ATF4, and downstream targets including CHOP/CHAC1/PPP1R15A/FGF21 in SPAX5 contexts. These may serve as candidate biomarkers for patient stratification or monitoring in future interventions targeting the ISR. (franchino2024sustainedoma1mediatedintegrated pages 1-2)

6) Human phenotypes and genotype–phenotype mapping (current 2024 view)

6.1 Dominant SCA28 (MIM#610246)

SCA28 is described as a slowly progressive cerebellar ataxia, typically with oculomotor abnormalities; heterozygous pathogenic variants are a primary genetic cause. (dastidar2024multifacetedrolesof pages 15-16, franchino2024sustainedoma1mediatedintegrated pages 1-2)

6.2 Dominant optic neuropathy: DOA12/OPA12 (MIM#618977)

Heterozygous variants (notably in ATPase/catalytic domains) are linked to dominant optic atrophy 12, and may overlap with additional ocular/mitochondrial phenotypes depending on variant and genetic context. (dastidar2024multifacetedrolesof pages 15-16, franchino2024sustainedoma1mediatedintegrated pages 1-2)

6.3 Recessive early-onset spastic ataxia-neuropathy: SPAX5 / spastic ataxia type 5

Biallelic loss-of-function variants cause a severe childhood-onset neurodegenerative disorder including cerebellar ataxia, spasticity, dystonia, neuropathy, and potentially myoclonic epilepsy. (dastidar2024multifacetedrolesof pages 15-16, franchino2024sustainedoma1mediatedintegrated pages 1-2)

7) Expert opinion / analysis (authoritative perspectives grounded in evidence)

AFG3L2 is increasingly viewed as a regulated remodeling protease, not merely a constitutive “garbage disposal.” Evidence includes stress- and nutrient-state regulation (HIF1α–mTORC1 axis) with broad substrate turnover shifts under hypoxia. (chandragiri2024afg3l2mediatedproteolysisrestricts pages 9-13)
Distinct mechanistic “modules” connect AFG3L2 dysfunction to disease:
proteotoxic stress → OMA1 activation → OPA1 processing → mitochondrial fragmentation → ISR activation, with ISR shown to be beneficial when pharmacologically potentiated in SPAX5 models. (franchino2024sustainedoma1mediatedintegrated pages 1-2)
metabolite sensing/feedback → GSH-dependent control of SLC25A39 abundance, linking AFG3L2 to redox and Fe–S-linked metabolism. (liu2023autoregulatorycontrolof pages 3-4)

Together these suggest that therapeutic strategies may need to be tailored to the dominant mechanistic axis in a given genotype/phenotype (e.g., ISR modulation for SPAX5-like biallelic loss; metabolic/proteostasis stabilization approaches for other contexts). (liu2023autoregulatorycontrolof pages 3-4, franchino2024sustainedoma1mediatedintegrated pages 1-2)

8) Relevant statistics and quantitative data (from recent studies)

SLC25A39 protein half-life: ~15 min at baseline; stabilized to >300 min under mitochondrial GSH depletion (MitoCHAC1 strategy) and rapidly degraded upon GSH supplementation, implicating AFG3L2-mediated control. (Nov 2023; https://doi.org/10.1126/science.adf4154) (liu2023autoregulatorycontrolof pages 3-4)
Scale of AFG3L2-dependent proteome remodeling in hypoxia: proteomics reported 38 proteins reduced with amino-acid starvation and 72 proteins decreased in hypoxia in an AFG3L2-dependent manner, emphasizing broad but enriched targeting of mitochondrial gene-expression machinery and related pathways. (Sep 2024; https://doi.org/10.1101/2024.09.27.615438) (chandragiri2024afg3l2mediatedproteolysisrestricts pages 9-13)
Genetic variant-type distribution for SCA28: a 2024 diagnostic review table reports >99% of reported SCA28 cases involve SNVs/small intragenic indels, with monoallelic deletion/duplication described as extremely rare, informing testing strategy. (Feb 2024; https://doi.org/10.3389/fnint.2023.1275794) (lopergolo2024autosomalrecessivecerebellar pages 4-5)

9) Evidence map (structured summary)

The following table consolidates the main functional and translational points (complex identity, substrates, regulation, diseases) with DOI URLs.

Category	Specific detail	Evidence type (review/primary)	Key recent citation(s) with year + DOI URL
Protein/complex	AFG3L2 = human mitochondrial inner-membrane m-AAA protease subunit (UniProt Q9Y4W6); assembles as homo-hexamers or hetero-hexamers with SPG7/paraplegin to form the matrix-facing m-AAA protease complex (franchino2024sustainedoma1mediatedintegrated pages 1-2, dastidar2024multifacetedrolesof pages 1-2, dastidar2024multifacetedrolesof pages 2-5)	Review + primary	Dastidar et al., 2024, Mol Neurobiol, https://doi.org/10.1007/s12035-023-03768-z; Franchino et al., 2024, Brain, https://doi.org/10.1093/brain/awad340
Localization/topology	Inner mitochondrial membrane (IMM), catalytic sites/AAA+ module facing the matrix; IM-anchored metalloprotease involved in protein quality control and mitochondrial biogenesis (franchino2024sustainedoma1mediatedintegrated pages 1-2, khalimonchuk2023moleculardeterminantsof pages 6-8, chandragiri2024afg3l2mediatedproteolysisrestricts pages 1-5)	Review + primary	Khalimonchuk & Becker, 2023, Antioxid Redox Signal, https://doi.org/10.1089/ars.2022.0124; Franchino et al., 2024, Brain, https://doi.org/10.1093/brain/awad340
Catalytic activities	Dual function: AAA+ ATPase/unfoldase-translocase plus zinc metalloprotease; ATP-driven substrate engagement/translocation feeds substrates to a C-terminal Zn-dependent protease site (dastidar2024multifacetedrolesof pages 1-2, dastidar2024multifacetedrolesof pages 2-5, khalimonchuk2023moleculardeterminantsof pages 6-8)	Review	Dastidar et al., 2024, Mol Neurobiol, https://doi.org/10.1007/s12035-023-03768-z; Khalimonchuk & Becker, 2023, Antioxid Redox Signal, https://doi.org/10.1089/ars.2022.0124
Substrate: SLC25A39	SLC25A39 glutathione transporter is an experimentally supported AFG3L2 substrate; mitochondrial GSH depletion stabilizes SLC25A39 by reducing AFG3L2-dependent turnover, whereas GSH supplementation restores rapid degradation (liu2023autoregulatorycontrolof pages 3-4, chandragiri2024afg3l2mediatedproteolysisrestricts pages 1-5, chandragiri2024afg3l2mediatedproteolysisrestricts pages 5-9)	Primary + review	Liu et al., 2023, Science, https://doi.org/10.1126/science.adf4154; Chandragiri et al., 2024, bioRxiv, https://doi.org/10.1101/2024.09.27.615438
Substrate: MRPL32 / bL32m	AFG3L2/m-AAA supports biogenesis/processing of mitochondrial ribosomal bL32m (MRPL32), linking proteolysis to mitochondrial ribosome assembly and protein synthesis (chandragiri2024afg3l2mediatedproteolysisrestricts pages 1-5, dastidar2024multifacetedrolesof pages 7-9, khalimonchuk2023moleculardeterminantsof pages 6-8)	Review + primary	Khalimonchuk & Becker, 2023, Antioxid Redox Signal, https://doi.org/10.1089/ars.2022.0124; Chandragiri et al., 2024, bioRxiv, https://doi.org/10.1101/2024.09.27.615438
Substrate: EMRE	AFG3L2/m-AAA contributes to EMRE maturation/turnover, thereby regulating the mitochondrial calcium uniporter machinery and mitochondrial Ca²⁺ handling (chandragiri2024afg3l2mediatedproteolysisrestricts pages 1-5, dastidar2024multifacetedrolesof pages 7-9, khalimonchuk2023moleculardeterminantsof pages 6-8)	Review + primary	Khalimonchuk & Becker, 2023, Antioxid Redox Signal, https://doi.org/10.1089/ars.2022.0124; Chandragiri et al., 2024, bioRxiv, https://doi.org/10.1101/2024.09.27.615438
Substrate: TIMMDC1	TIMMDC1, a complex I assembly factor, is degraded by AFG3L2, linking m-AAA proteolysis to respiratory-chain assembly control (chandragiri2024afg3l2mediatedproteolysisrestricts pages 1-5, chandragiri2024afg3l2mediatedproteolysisrestricts pages 5-9)	Primary	Chandragiri et al., 2024, bioRxiv, https://doi.org/10.1101/2024.09.27.615438
Substrate/regulator: TMBIM5 (GHITM)	TMBIM5/GHITM is both an AFG3L2 substrate and an inhibitor/modulator of AFG3L2, connecting the protease to mitochondrial Ca²⁺/H⁺ homeostasis and stress adaptation (chandragiri2024afg3l2mediatedproteolysisrestricts pages 1-5, chandragiri2024afg3l2mediatedproteolysisrestricts pages 13-16)	Primary	Chandragiri et al., 2024, bioRxiv, https://doi.org/10.1101/2024.09.27.615438
Substrates: RNA metabolism factors	Recent proteomics identified AFG3L2 substrates in mitochondrial RNA metabolism/gene expression, including LRPPRC, SLIRP, MTPAP, POLRMT, TFB2M, DHX30, GRSF1, plus import factors (PAM16, DNAJC15, TIMM17A), especially under hypoxia (chandragiri2024afg3l2mediatedproteolysisrestricts pages 13-16, chandragiri2024afg3l2mediatedproteolysisrestricts pages 5-9, chandragiri2024afg3l2mediatedproteolysisrestricts pages 9-13)	Primary	Chandragiri et al., 2024, bioRxiv, https://doi.org/10.1101/2024.09.27.615438
Regulatory pathway: GSH-dependent dissociation	Mitochondrial glutathione status regulates AFG3L2–SLC25A39 interaction: low matrix GSH promotes SLC25A39 stabilization by diminishing AFG3L2-mediated degradation, forming an autoregulatory feedback loop for mitochondrial GSH import (liu2023autoregulatorycontrolof pages 3-4)	Primary	Liu et al., 2023, Science, https://doi.org/10.1126/science.adf4154
Regulatory pathway: Hypoxia / HIF1α–mTORC1	AFG3L2 proteolysis is activated in hypoxia along a HIF1α–mTORC1 axis; mTORC1 inhibition or amino-acid starvation increases turnover of multiple AFG3L2 substrates, whereas constitutive mTORC1 activity stabilizes them (chandragiri2024afg3l2mediatedproteolysisrestricts pages 1-5, chandragiri2024afg3l2mediatedproteolysisrestricts pages 13-16, chandragiri2024afg3l2mediatedproteolysisrestricts pages 9-13)	Primary	Chandragiri et al., 2024, bioRxiv, https://doi.org/10.1101/2024.09.27.615438
Regulatory pathway: PHB scaffold	The prohibitin (PHB) membrane scaffold complex associates with m-AAA protease and can modulate substrate-specific AFG3L2 activity, including in hypoxic remodeling of the mitochondrial proteome (chandragiri2024afg3l2mediatedproteolysisrestricts pages 13-16)	Primary	Chandragiri et al., 2024, bioRxiv, https://doi.org/10.1101/2024.09.27.615438
Regulatory pathway: OMA1–DELE1–HRI ISR	In AFG3L2 deficiency/mutation, mitochondrial proteotoxic stress causes OMA1 overactivation, excessive OPA1 processing, mitochondrial fragmentation, and activation of the OMA1–DELE1–HRI integrated stress response (ISR) with increased eIF2α phosphorylation and ATF4 signaling (franchino2024sustainedoma1mediatedintegrated pages 1-2)	Primary	Franchino et al., 2024, Brain, https://doi.org/10.1093/brain/awad340
Human disease: SCA28	Spinocerebellar ataxia type 28 (SCA28): typically autosomal dominant, usually from heterozygous AFG3L2 variants, characterized by slowly progressive gait/limb ataxia with frequent oculomotor abnormalities (dastidar2024multifacetedrolesof pages 15-16, dastidar2024multifacetedrolesof pages 10-11, lopergolo2024autosomalrecessivecerebellar pages 4-5, franchino2024sustainedoma1mediatedintegrated pages 1-2)	Review + primary	Franchino et al., 2024, Brain, https://doi.org/10.1093/brain/awad340; Dastidar et al., 2024, Mol Neurobiol, https://doi.org/10.1007/s12035-023-03768-z
Human disease: DOA12 / OPA12	Dominant optic atrophy 12 (DOA12/OPA12): generally autosomal dominant, associated especially with heterozygous ATPase- or catalytic-domain variants; may overlap with ophthalmoplegia and broader mitochondrial optic neuropathy phenotypes (dastidar2024multifacetedrolesof pages 15-16, dastidar2024multifacetedrolesof pages 13-15, franchino2024sustainedoma1mediatedintegrated pages 1-2)	Review + primary	Franchino et al., 2024, Brain, https://doi.org/10.1093/brain/awad340; Dastidar et al., 2024, Mol Neurobiol, https://doi.org/10.1007/s12035-023-03768-z
Human disease: SPAX5	Spastic ataxia type 5 / early-onset spastic ataxia-neuropathy syndrome (SPAX5): autosomal recessive, caused by biallelic AFG3L2 variants; severe childhood-onset phenotype with cerebellar ataxia, spasticity, dystonia, neuropathy, and in some cases myoclonic epilepsy (dastidar2024multifacetedrolesof pages 15-16, lopergolo2024autosomalrecessivecerebellar pages 4-5, dastidar2024multifacetedrolesof pages 13-15, franchino2024sustainedoma1mediatedintegrated pages 1-2)	Review + primary	Franchino et al., 2024, Brain, https://doi.org/10.1093/brain/awad340; Dastidar et al., 2024, Mol Neurobiol, https://doi.org/10.1007/s12035-023-03768-z
Therapeutic/diagnostic implications	Current clinical use is mainly genetic diagnosis/variant interpretation (NGS panels, exome-based workup for ataxia/optic neuropathy). Preclinical 2024 evidence suggests ISR potentiation with Sephin-1 can improve SPAX5 cellular and mouse phenotypes; molecular readouts include eIF2α phosphorylation, ATF4 targets, CHOP/CHAC1/FGF21 (dastidar2024multifacetedrolesof pages 15-16, dastidar2024multifacetedrolesof pages 10-11, franchino2024sustainedoma1mediatedintegrated pages 1-2)	Review + primary	Franchino et al., 2024, Brain, https://doi.org/10.1093/brain/awad340; Dastidar et al., 2024, Mol Neurobiol, https://doi.org/10.1007/s12035-023-03768-z

Table: This table condenses the core functional annotation of human AFG3L2, including complex identity, localization, catalytic mechanism, experimentally supported substrates, regulatory pathways, and associated human diseases. It is useful as a quick-reference map linking molecular function to disease relevance and recent literature.

10) Limitations of the current evidence base (important for annotation quality)

Some mechanistic claims in the 2024 hypoxia study are from a bioRxiv preprint and therefore not yet peer-reviewed; the results are still useful as “latest research” but should be treated cautiously until validated. (chandragiri2024afg3l2mediatedproteolysisrestricts pages 1-5, chandragiri2024afg3l2mediatedproteolysisrestricts pages 9-13)
AFG3L2-disease epidemiology (penetrance, population prevalence of SCA28/DOA12/SPAX5 specifically) was not directly available in the retrieved 2023–2024 sources; the report therefore focuses on mechanistic and diagnostic implementation evidence rather than attempting unsupported prevalence estimates. (dastidar2024multifacetedrolesof pages 15-16, lopergolo2024autosomalrecessivecerebellar pages 4-5)

Key recent sources (URLs + publication timing)

Liu et al., Science, Nov 2023: https://doi.org/10.1126/science.adf4154 (liu2023autoregulatorycontrolof pages 3-4)
Khalimonchuk & Becker, Antioxidants & Redox Signaling, May 2023: https://doi.org/10.1089/ars.2022.0124 (khalimonchuk2023moleculardeterminantsof pages 6-8)
Franchino et al., Brain, Oct 2024: https://doi.org/10.1093/brain/awad340 (franchino2024sustainedoma1mediatedintegrated pages 1-2)
Dastidar et al., Molecular Neurobiology, 2024 (online; issue cites Nov 2024): https://doi.org/10.1007/s12035-023-03768-z (dastidar2024multifacetedrolesof pages 1-2)
Chandragiri et al., bioRxiv preprint, Sep 2024: https://doi.org/10.1101/2024.09.27.615438 (chandragiri2024afg3l2mediatedproteolysisrestricts pages 9-13)
Lopergolo et al., Frontiers in Integrative Neuroscience, Feb 2024: https://doi.org/10.3389/fnint.2023.1275794 (lopergolo2024autosomalrecessivecerebellar pages 4-5)

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(lopergolo2024autosomalrecessivecerebellar pages 4-5): Diego Lopergolo, Francesca Rosini, Elena Pretegiani, Alessia Bargagli, Valeria Serchi, and Alessandra Rufa. Autosomal recessive cerebellar ataxias: a diagnostic classification approach according to ocular features. Frontiers in Integrative Neuroscience, Feb 2024. URL: https://doi.org/10.3389/fnint.2023.1275794, doi:10.3389/fnint.2023.1275794. This article has 10 citations.
(dastidar2024multifacetedrolesof pages 15-16): Ranita Ghosh Dastidar, Saradindu Banerjee, Piyush Behari Lal, and Somasish Ghosh Dastidar. Multifaceted roles of afg3l2, a mitochondrial atpase in relation to neurological disorders. Molecular Neurobiology, 61:3788-3808, Nov 2024. URL: https://doi.org/10.1007/s12035-023-03768-z, doi:10.1007/s12035-023-03768-z. This article has 19 citations and is from a peer-reviewed journal.
(dastidar2024multifacetedrolesof pages 10-11): Ranita Ghosh Dastidar, Saradindu Banerjee, Piyush Behari Lal, and Somasish Ghosh Dastidar. Multifaceted roles of afg3l2, a mitochondrial atpase in relation to neurological disorders. Molecular Neurobiology, 61:3788-3808, Nov 2024. URL: https://doi.org/10.1007/s12035-023-03768-z, doi:10.1007/s12035-023-03768-z. This article has 19 citations and is from a peer-reviewed journal.
(dastidar2024multifacetedrolesof pages 7-9): Ranita Ghosh Dastidar, Saradindu Banerjee, Piyush Behari Lal, and Somasish Ghosh Dastidar. Multifaceted roles of afg3l2, a mitochondrial atpase in relation to neurological disorders. Molecular Neurobiology, 61:3788-3808, Nov 2024. URL: https://doi.org/10.1007/s12035-023-03768-z, doi:10.1007/s12035-023-03768-z. This article has 19 citations and is from a peer-reviewed journal.
(dastidar2024multifacetedrolesof pages 13-15): Ranita Ghosh Dastidar, Saradindu Banerjee, Piyush Behari Lal, and Somasish Ghosh Dastidar. Multifaceted roles of afg3l2, a mitochondrial atpase in relation to neurological disorders. Molecular Neurobiology, 61:3788-3808, Nov 2024. URL: https://doi.org/10.1007/s12035-023-03768-z, doi:10.1007/s12035-023-03768-z. This article has 19 citations and is from a peer-reviewed journal.

Artifacts

Edison artifact artifact-00

Citations

liu2023autoregulatorycontrolof pages 3-4
lopergolo2024autosomalrecessivecerebellar pages 4-5
dastidar2024multifacetedrolesof pages 15-16
khalimonchuk2023moleculardeterminantsof pages 6-8
dastidar2024multifacetedrolesof pages 1-2
dastidar2024multifacetedrolesof pages 2-5
dastidar2024multifacetedrolesof pages 10-11
dastidar2024multifacetedrolesof pages 7-9
dastidar2024multifacetedrolesof pages 13-15
https://doi.org/10.1126/science.adf4154
https://doi.org/10.1093/brain/awad340
https://doi.org/10.1101/2024.09.27.615438
https://doi.org/10.3389/fnint.2023.1275794
https://doi.org/10.1007/s12035-023-03768-z;
https://doi.org/10.1089/ars.2022.0124;
https://doi.org/10.1089/ars.2022.0124
https://doi.org/10.1126/science.adf4154;
https://doi.org/10.1093/brain/awad340;
https://doi.org/10.1007/s12035-023-03768-z
https://doi.org/10.1093/brain/awad340,
https://doi.org/10.1007/s12035-023-03768-z,
https://doi.org/10.1126/science.adf4154,
https://doi.org/10.1101/2024.09.27.615438,
https://doi.org/10.1089/ars.2022.0124,
https://doi.org/10.3389/fnint.2023.1275794,

📚 Additional Documentation

Notes

(AFG3L2-notes.md)

AFG3L2 notes

2026-06-03 Proteostasis PN review

Falcon deep research completed for human AFG3L2/Q9Y4W6 and was used as a synthesis check against the cached GOA-linked literature. The report consistently identifies AFG3L2 as the human mitochondrial inner membrane m-AAA protease subunit, not a soluble matrix protease.

Literature synthesis

AFG3L2 is an m-AAA protease subunit anchored in the mitochondrial inner membrane, with the catalytic AAA+ ATPase and zinc metalloprotease modules exposed toward the matrix side. The topology point is important for PN projection: the protein acts on matrix-facing substrates but is itself an inner membrane protein PMID:31327635. Older biochemical work also recovered paraplegin and AFG3L2 in the membrane fraction PMID:14623864.

The core activity is ATP-dependent substrate unfolding/translocation coupled to metalloprotease cleavage. Structural work reports that AFG3L2 has features required for "ATP-dependent translocation to unfold and degrade targeted proteins" PMID:31327635, and biochemical work describes human AFG3L2 as an "ATP-fueled degradation" protease at the matrix face of the inner membrane PMID:29932645. ATP hydrolysis is a real catalytic activity, not just a binding annotation PMID:19748354.

The biological process center is mitochondrial substrate degradation and processing. AFG3L2 is required for mitochondrial protein quality control of newly synthesized or misassembled inner-membrane proteins PMID:26504172 and resolves MT-ATP6 insertion defects PMID:34718584. It also processes selected substrates such as MRPL32 PMID:29932645.

Several substrate-specific consequences are well supported but should be treated as non-core relative to the m-AAA protease function. AFG3L2/SPG7 degrade unassembled EMRE/SMDT1 to regulate MCU complex assembly and calcium import [PMID:27642048 "the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU"; PMID:28396416 "mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis"]. AFG3L2 also degrades SLC25A39 in a glutathione-sensitive feedback circuit [PMID:37917749 "Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2."; PMID:38157846 "mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1"].

PN projection evaluation

The PN projection proposed two AFG3L2 candidate additions from Mitochondrial proteostasis|Organelle-specific protein degradation|Matrix protease:

GO:0035694 mitochondrial protein catabolic process
GO:0005759 mitochondrial matrix

I accepted GO:0035694 mitochondrial protein catabolic process as a conservative NEW annotation. Existing GOA already has generic GO:0030163 protein catabolic process and generic GO:0006508 proteolysis; the literature supports a mitochondrial-specific degradation process, and the PN report itself states that "GO mitochondrial protein catabolic process is the conservative shared target."

I did not add GO:0005759 mitochondrial matrix. The PN class label "Matrix protease" reflects the side of the inner membrane where the catalytic domains face and where many substrates are exposed. It does not override the stronger cellular component evidence that AFG3L2 is an integral mitochondrial inner membrane protein. The safer cellular component remains GO:0005743 mitochondrial inner membrane, including is_active_in when available.

Annotation strategy

Generic proteolysis and protein catabolic process annotations were marked for replacement by GO:0035694 mitochondrial protein catabolic process. Broad membrane or mitochondrion cellular component annotations were marked for replacement by GO:0005743 mitochondrial inner membrane.

The protein binding IPI rows were treated as over-annotations. The reported interactions are real, but the generic MF term does not communicate AFG3L2 function. Where appropriate, the informative biology is captured by m-AAA complex, substrate degradation, mitochondrial calcium import regulation, glutathione-response biology, or mitochondrial protein quality control.

Pn Notes

(AFG3L2-pn-notes.md)

AFG3L2 PN Consistency Notes

Generated: 2026-06-18
Project: PROTEOSTASIS
Scope: PN consistency rereview against local AIGR review and available deep-research artifacts
UniProt: Q9Y4W6
AIGR review status: COMPLETE
Review batch: proteostasis-batch-2026-06-03 (PR 1345)
Batch change status: added

Source Files Checked

AIGR review YAML: present - genes/human/AFG3L2/AFG3L2-ai-review.yaml
AIGR review HTML: present - genes/human/AFG3L2/AFG3L2-ai-review.html
Gene notes: present - genes/human/AFG3L2/AFG3L2-notes.md
GOA TSV: present - genes/human/AFG3L2/AFG3L2-goa.tsv
UniProt record: present - genes/human/AFG3L2/AFG3L2-uniprot.txt
PN dossier: projects/PROTEOSTASIS/reports/phase1_dossiers/AFG3L2.md
PN consistency section: projects/PROTEOSTASIS/reports/phase1_dossiers/_sections/AFG3L2.md
PN projection report: projects/PROTEOSTASIS/reports/pn_projection/pn_projected_gene_go_summary.tsv
PN mapping audit: projects/PROTEOSTASIS/reports/pn_mapping_audit/current_mapping_scrutiny.tsv

Deep Research Files

genes/human/AFG3L2/AFG3L2-deep-research-falcon.md

AIGR Review Snapshot

Description: AFG3L2 is a mitochondrial inner membrane m-AAA protease subunit with AAA+ ATPase and zinc metalloendopeptidase domains exposed to the matrix side of the inner membrane. It assembles as AFG3L2 homohexamers and as AFG3L2-SPG7 heterohexamers that use ATP hydrolysis to unfold, translocate, and cleave mitochondrial substrates. Its major roles include protein quality control of newly synthesized or misassembled inner-membrane proteins, processing of selected mitochondrial proteins such as MRPL32 and PINK1, and regulatory degradation of substrates including EMRE/SMDT1, SLC25A39, SLC25A45, and TMBIM5/GHITM. Through these proteolytic activities AFG3L2 supports mitochondrial respiratory-chain assembly, calcium uniporter regulation, mitochondrial glutathione homeostasis, mitochondrial morphology, and neuronal maintenance.
Existing/core annotation action counts: ACCEPT: 43; KEEP_AS_NON_CORE: 11; MARK_AS_OVER_ANNOTATED: 6; MODIFY: 17; NEW: 1

PN Consistency Summary

Consistency: Deep research (falcon), review YAML, and PN annotation agree on the core picture: AFG3L2 is the m-AAA inner-membrane AAA+/M41 zinc metalloprotease performing mitochondrial protein QC, processing (MRPL32), and regulated degradation (EMRE, SLC25A39/45, PINK1, TMBIM5). One deliberate, well-flagged divergence: the PN group projects GO:0005759 mitochondrial matrix as the localization target, but the review rejects this (AFG3L2 is an integral inner-membrane protein with matrix-facing catalytic domains) and keeps GO:0005743 mitochondrial inner membrane. The NEW row's reason explicitly states the matrix projection is not accepted. No contradiction beyond this intentional correction.
PN story / NEW pressure: PN class target GO:0035694 mitochondrial protein catabolic process (verified real, non-obsolete) is added as a NEW (IC) annotation and used to MODIFY the generic GO:0006508 proteolysis / GO:0030163 protein catabolic process rows. Defensible and conservative — directly supported by SLC25A39 degradation papers (PMID:37917749, 38157846). Verdict: ADD (already implemented in review).
Evidence alignment: PN dossier carries no reference titles; review is densely evidenced (PMID:31327635, 29932645, 19748354, 27642048, 28396416, 37917749, 38157846, 41075794). PN projection TSV is cited as supporting file for GO:0035694. No PMID-level conflicts.
Verdict: Consistent; PN GO:0035694 correctly adopted as NEW; PN matrix (GO:0005759) projection correctly overruled at gene level. Recommended edits: none required. Optional [MAP]: flag mitochondrial-proteostasis "Matrix protease" group GO:0005759 as too specific for inner-membrane matrix-facing proteases (consider GO:0005743 or no_mapping).

Full Consistency Review

UniProt: Q9Y4W6 · batch: proteostasis-batch-2026-06-03 · review status: COMPLETE
PN placement: Mitochondrial proteostasis|Organelle-specific protein degradation|Matrix protease ; PN-node mapping: group mapped ok_for_propagation GO:0005759 mitochondrial matrix; class mapped GO:0035694 mitochondrial protein catabolic process; branch no_mapping.
Consistency: Deep research (falcon), review YAML, and PN annotation agree on the core picture: AFG3L2 is the m-AAA inner-membrane AAA+/M41 zinc metalloprotease performing mitochondrial protein QC, processing (MRPL32), and regulated degradation (EMRE, SLC25A39/45, PINK1, TMBIM5). One deliberate, well-flagged divergence: the PN group projects GO:0005759 mitochondrial matrix as the localization target, but the review rejects this (AFG3L2 is an integral inner-membrane protein with matrix-facing catalytic domains) and keeps GO:0005743 mitochondrial inner membrane. The NEW row's reason explicitly states the matrix projection is not accepted. No contradiction beyond this intentional correction.
PN story / NEW pressure: PN class target GO:0035694 mitochondrial protein catabolic process (verified real, non-obsolete) is added as a NEW (IC) annotation and used to MODIFY the generic GO:0006508 proteolysis / GO:0030163 protein catabolic process rows. Defensible and conservative — directly supported by SLC25A39 degradation papers (PMID:37917749, 38157846). Verdict: ADD (already implemented in review).
Mapping strategy: Gene refines, does not change, the node. The class→GO:0035694 mapping is correct and adopted. The group→GO:0005759 matrix mapping is too specific/wrong-compartment for AFG3L2; review's rejection is sound (matrix-facing topology ≠ matrix residence).
Evidence alignment: PN dossier carries no reference titles; review is densely evidenced (PMID:31327635, 29932645, 19748354, 27642048, 28396416, 37917749, 38157846, 41075794). PN projection TSV is cited as supporting file for GO:0035694. No PMID-level conflicts.
Verdict: Consistent; PN GO:0035694 correctly adopted as NEW; PN matrix (GO:0005759) projection correctly overruled at gene level. Recommended edits: none required. Optional [MAP]: flag mitochondrial-proteostasis "Matrix protease" group GO:0005759 as too specific for inner-membrane matrix-facing proteases (consider GO:0005743 or no_mapping).

PN Dossier Context

review_batch: proteostasis-batch-2026-06-03
review_yaml: genes/human/AFG3L2/AFG3L2-ai-review.yaml
PN workbook rows: 1

PN row 1: Mitochondrial proteostasis | Organelle-specific protein degradation | Matrix protease

UniProt: Q9Y4W6
In branches: MI
PN-node mapping records (path + ancestors):
- [group] Mitochondrial proteostasis|Organelle-specific protein degradation|Matrix protease
  status=mapped scope=ok_for_propagation_to_go GO=[GO:0005759 mitochondrial matrix]
  rationale: This PN group identifies matrix-local protease systems. The source is a compartmental proteostasis bucket, so the mitochondrial matrix cellular-component term is the conservative propagation target.
- [class] Mitochondrial proteostasis|Organelle-specific protein degradation
  status=mapped scope=ok_for_propagation_to_go GO=[GO:0035694 mitochondrial protein catabolic process]
  rationale: This PN class groups mitochondrial protein-degradation pathways. GO mitochondrial protein catabolic process is the conservative shared target.
- [branch] Mitochondrial proteostasis
  status=no_mapping scope= GO=[]
  rationale: Reviewed as a top-level PN branch. This is a systems/taxonomy umbrella, not a direct GO assertion; narrower child curations carry any propagating GO mappings.

Projected GO annotations (2)

GO:0035694 mitochondrial protein catabolic process | scope=ok_for_propagation_to_go | goa_status=more_specific_than_existing_goa | from=Mitochondrial proteostasis|Organelle-specific protein degradation
GO:0005759 mitochondrial matrix | scope=ok_for_propagation_to_go | goa_status=more_specific_than_existing_goa | from=Mitochondrial proteostasis|Organelle-specific protein degradation|Matrix protease

Note

This file is generated from the current PROTEOSTASIS phase-1 dossier and local gene-review artifacts. Edit the source review, PN mapping, or dossier rather than this generated note when correcting the underlying curation.

📄 View Raw YAML

id: Q9Y4W6
gene_symbol: AFG3L2
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: AFG3L2 is a mitochondrial inner membrane m-AAA protease subunit with AAA+ ATPase and zinc metalloendopeptidase domains exposed to the matrix side of the inner membrane. It assembles as AFG3L2 homohexamers and as AFG3L2-SPG7 heterohexamers that use ATP hydrolysis to unfold, translocate, and cleave mitochondrial substrates. Its major roles include protein quality control of newly synthesized or misassembled inner-membrane proteins, processing of selected mitochondrial proteins such as MRPL32 and PINK1, and regulatory degradation of substrates including EMRE/SMDT1, SLC25A39, SLC25A45, and TMBIM5/GHITM. Through these proteolytic activities AFG3L2 supports mitochondrial respiratory-chain assembly, calcium uniporter regulation, mitochondrial glutathione homeostasis, mitochondrial morphology, and neuronal maintenance.
existing_annotations:
- term:
    id: GO:0034982
    label: mitochondrial protein processing
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  supporting_entities:
  - FB:FBgn0036702
  - MGI:MGI:1916847
  - MGI:MGI:1928277
  - PANTHER:PTN000554085
  - UniProtKB:Q9UQ90
  - UniProtKB:Q9Y4W6
  - WB:WBGene00004978
  review:
    summary: AFG3L2 directly processes mitochondrial substrates, including MRPL32 and multiple inner membrane proteins/carriers.
    action: ACCEPT
    reason: Mitochondrial protein processing is a core biological role of the m-AAA protease alongside degradative quality control.
    supported_by:
    - reference_id: PMID:29932645
      supporting_text: conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form
    - reference_id: PMID:41075794
      supporting_text: SLC25A45-FLAG levels only increased in cells treated with siRNA targeting AFG3L2
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
- term:
    id: GO:0005745
    label: m-AAA complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: part_of
  supporting_entities:
  - FB:FBgn0024992
  - FB:FBgn0036702
  - MGI:MGI:1916847
  - MGI:MGI:1928277
  - MGI:MGI:2385906
  - PANTHER:PTN000554085
  - SGD:S000000819
  - SGD:S000004695
  - UniProtKB:Q9UQ90
  - UniProtKB:Q9Y4W6
  review:
    summary: AFG3L2 is a constituent of the mitochondrial m-AAA protease complex, as homohexamers and as heterohexamers with SPG7.
    action: ACCEPT
    reason: The m-AAA complex is the correct cellular component context for AFG3L2 protease function.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7)
    - reference_id: PMID:14623864
      supporting_text: paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane
- term:
    id: GO:0004222
    label: metalloendopeptidase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  supporting_entities:
  - PANTHER:PTN008683692
  - UniProtKB:Q9UQ90
  - UniProtKB:Q9Y4W6
  review:
    summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit.
    action: ACCEPT
    reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
- term:
    id: GO:0004176
    label: ATP-dependent peptidase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  supporting_entities:
  - InterPro:IPR000642
  - InterPro:IPR005936
  - InterPro:IPR011546
  - InterPro:IPR037219
  review:
    summary: ATP-dependent peptidase activity accurately combines the ATPase and protease aspects of AFG3L2 function.
    action: ACCEPT
    reason: The m-AAA protease uses ATP hydrolysis to unfold/translocate substrates and protease active sites to degrade them.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
    - reference_id: PMID:19748354
      supporting_text: we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes
- term:
    id: GO:0004222
    label: metalloendopeptidase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  supporting_entities:
  - InterPro:IPR000642
  - InterPro:IPR005936
  - InterPro:IPR011546
  - InterPro:IPR037219
  review:
    summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit.
    action: ACCEPT
    reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  supporting_entities:
  - InterPro:IPR000642
  - InterPro:IPR003959
  - InterPro:IPR003960
  - InterPro:IPR011546
  - InterPro:IPR037219
  review:
    summary: ATP binding is a true domain-associated property, but ATP hydrolysis is the informative catalytic annotation.
    action: KEEP_AS_NON_CORE
    reason: Keep as a non-core molecular feature; core function should emphasize ATP hydrolysis and ATP-dependent peptidase activity.
    supported_by:
    - reference_id: PMID:19748354
      supporting_text: we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes
    - reference_id: PMID:31327635
      supporting_text: ATP-dependent translocation to unfold and degrade targeted proteins
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: located_in
  supporting_entities:
  - UniProtKB:Q8JZQ2
  - ensembl:ENSMUSP00000025408
  - UniProtKB-SubCell:SL-0168
  review:
    summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side.
    action: ACCEPT
    reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0006508
    label: proteolysis
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  supporting_entities:
  - ARBA:ARBA00026291
  - InterPro:IPR000642
  - InterPro:IPR037219
  review:
    summary: Generic proteolysis is correct but underspecified for the mitochondrial m-AAA protease role.
    action: MODIFY
    reason: The evidence supports mitochondrial substrate degradation and protein quality control, not merely generic proteolysis.
    proposed_replacement_terms:
    - id: GO:0035694
      label: mitochondrial protein catabolic process
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
    - reference_id: file:projects/PROTEOSTASIS/reports/pn_projection/pn_projected_annotations.tsv
      supporting_text: This PN class groups mitochondrial protein-degradation pathways. GO mitochondrial protein catabolic process is the conservative shared target.
- term:
    id: GO:0008270
    label: zinc ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  supporting_entities:
  - InterPro:IPR011546
  review:
    summary: Zinc binding is supported by the M41 metalloprotease active site but is not itself the core function.
    action: KEEP_AS_NON_CORE
    reason: Keep as a cofactor/domain feature and emphasize metalloendopeptidase activity as the core molecular function.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
- term:
    id: GO:0016020
    label: membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: located_in
  supporting_entities:
  - InterPro:IPR005936
  - InterPro:IPR011546
  review:
    summary: Membrane localization is correct but too broad.
    action: MODIFY
    reason: AFG3L2 is specifically an integral mitochondrial inner membrane protein.
    proposed_replacement_terms:
    - id: GO:0005743
      label: mitochondrial inner membrane
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  supporting_entities:
  - InterPro:IPR003959
  - InterPro:IPR003960
  - RHEA:13065
  review:
    summary: ATP hydrolysis is a core motor activity of the AAA+ ring that powers substrate unfolding and translocation.
    action: ACCEPT
    reason: This is directly supported by m-AAA ATPase assays and AFG3L2 structural work tying ATP-dependent translocation to substrate degradation.
    supported_by:
    - reference_id: PMID:19748354
      supporting_text: we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes
    - reference_id: PMID:31327635
      supporting_text: ATP-dependent translocation to unfold and degrade targeted proteins
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32814053
  qualifier: enables
  supporting_entities:
  - UniProtKB:P42858
  review:
    summary: The IPI row records binding to UniProtKB:P42858, but protein binding is too generic to describe AFG3L2 function.
    action: MARK_AS_OVER_ANNOTATED
    reason: Specific interactions should be interpreted through m-AAA complex membership, substrate degradation, calcium regulation, or other informative process terms rather than the generic protein binding MF term.
    supported_by:
    - reference_id: PMID:32814053
      supporting_text: Interactome maps are valuable resources to elucidate protein function and disease mechanisms.
- term:
    id: GO:0005745
    label: m-AAA complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: part_of
  supporting_entities:
  - ARBA:ARBA00088390
  - UniProtKB:Q8JZQ2
  - ensembl:ENSMUSP00000025408
  review:
    summary: AFG3L2 is a constituent of the mitochondrial m-AAA protease complex, as homohexamers and as heterohexamers with SPG7.
    action: ACCEPT
    reason: The m-AAA complex is the correct cellular component context for AFG3L2 protease function.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7)
    - reference_id: PMID:14623864
      supporting_text: paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane
- term:
    id: GO:0008237
    label: metallopeptidase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: enables
  supporting_entities:
  - UniProtKB:Q8JZQ2
  - ensembl:ENSMUSP00000025408
  review:
    summary: The annotation is directionally correct but too broad for AFG3L2.
    action: MODIFY
    reason: AFG3L2 is specifically supported as a metalloendopeptidase/m-AAA protease; use the more precise metalloendopeptidase activity term.
    proposed_replacement_terms:
    - id: GO:0004222
      label: metalloendopeptidase activity
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
- term:
    id: GO:0016485
    label: protein processing
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  supporting_entities:
  - UniProtKB:Q8JZQ2
  - ensembl:ENSMUSP00000025408
  review:
    summary: Protein processing is true but should be represented with the existing mitochondrial protein processing term.
    action: MODIFY
    reason: AFG3L2 processing events occur in mitochondria and are already captured more specifically by mitochondrial protein processing.
    proposed_replacement_terms:
    - id: GO:0034982
      label: mitochondrial protein processing
    supported_by:
    - reference_id: PMID:29932645
      supporting_text: conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form
    - reference_id: PMID:41075794
      supporting_text: SLC25A45-FLAG levels only increased in cells treated with siRNA targeting AFG3L2
- term:
    id: GO:0016540
    label: protein autoprocessing
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  supporting_entities:
  - UniProtKB:Q8JZQ2
  - ensembl:ENSMUSP00000025408
  review:
    summary: Autoprocessing of the imported precursor is described for AFG3L2, but it is ancillary to the mature protease role.
    action: KEEP_AS_NON_CORE
    reason: Retain as non-core because the main biological function is degradation/processing of mitochondrial substrates.
    supported_by:
    - reference_id: file:human/AFG3L2/AFG3L2-uniprot.txt
      supporting_text: autocatalytic proteolytic processing to generate the proteolytically active mature form
- term:
    id: GO:0051604
    label: protein maturation
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  supporting_entities:
  - ARBA:ARBA00026902
  - UniProtKB:Q8JZQ2
  - ensembl:ENSMUSP00000025408
  review:
    summary: Protein maturation is true for selected substrates but too generic.
    action: MODIFY
    reason: The evidence points to mitochondrial protein processing/maturation, especially MRPL32 and related mitochondrial substrates.
    proposed_replacement_terms:
    - id: GO:0034982
      label: mitochondrial protein processing
    supported_by:
    - reference_id: PMID:29932645
      supporting_text: conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form
    - reference_id: PMID:41075794
      supporting_text: SLC25A45-FLAG levels only increased in cells treated with siRNA targeting AFG3L2
- term:
    id: GO:0110097
    label: regulation of calcium import into the mitochondrion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  supporting_entities:
  - UniProtKB:Q8JZQ2
  - ensembl:ENSMUSP00000025408
  review:
    summary: AFG3L2 regulates mitochondrial calcium import by degrading unassembled EMRE before MCU complex assembly.
    action: KEEP_AS_NON_CORE
    reason: This is a supported substrate-specific consequence of m-AAA proteolysis, but not the central gene-level function.
    supported_by:
    - reference_id: PMID:27642048
      supporting_text: the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU
    - reference_id: PMID:28396416
      supporting_text: mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  qualifier: located_in
  review:
    summary: Mitochondrial localization is correct but less specific than the established inner-membrane localization.
    action: MODIFY
    reason: The earliest localization work supports mitochondria, and later biochemical/structural work resolves AFG3L2 to the mitochondrial inner membrane.
    proposed_replacement_terms:
    - id: GO:0005743
      label: mitochondrial inner membrane
    supported_by:
    - reference_id: PMID:10395799
      supporting_text: Immunofluorescence studies revealed that AFG3L2 and paraplegin share a similar expression pattern and the same subcellular localization, the mitochondrial compartment.
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0004222
    label: metalloendopeptidase activity
  evidence_type: IMP
  original_reference_id: PMID:41075794
  qualifier: enables
  review:
    summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit.
    action: ACCEPT
    reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
- term:
    id: GO:0034982
    label: mitochondrial protein processing
  evidence_type: IMP
  original_reference_id: PMID:41075794
  qualifier: involved_in
  review:
    summary: AFG3L2 directly processes mitochondrial substrates, including MRPL32 and multiple inner membrane proteins/carriers.
    action: ACCEPT
    reason: Mitochondrial protein processing is a core biological role of the m-AAA protease alongside degradative quality control.
    supported_by:
    - reference_id: PMID:29932645
      supporting_text: conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form
    - reference_id: PMID:41075794
      supporting_text: SLC25A45-FLAG levels only increased in cells treated with siRNA targeting AFG3L2
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: IDA
  original_reference_id: PMID:31327635
  qualifier: located_in
  review:
    summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side.
    action: ACCEPT
    reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0005745
    label: m-AAA complex
  evidence_type: IPI
  original_reference_id: PMID:31327635
  qualifier: part_of
  review:
    summary: AFG3L2 is a constituent of the mitochondrial m-AAA protease complex, as homohexamers and as heterohexamers with SPG7.
    action: ACCEPT
    reason: The m-AAA complex is the correct cellular component context for AFG3L2 protease function.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7)
    - reference_id: PMID:14623864
      supporting_text: paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane
- term:
    id: GO:0034982
    label: mitochondrial protein processing
  evidence_type: IDA
  original_reference_id: PMID:31327635
  qualifier: involved_in
  review:
    summary: AFG3L2 directly processes mitochondrial substrates, including MRPL32 and multiple inner membrane proteins/carriers.
    action: ACCEPT
    reason: Mitochondrial protein processing is a core biological role of the m-AAA protease alongside degradative quality control.
    supported_by:
    - reference_id: PMID:29932645
      supporting_text: conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form
    - reference_id: PMID:41075794
      supporting_text: SLC25A45-FLAG levels only increased in cells treated with siRNA targeting AFG3L2
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HTP
  original_reference_id: PMID:34800366
  qualifier: located_in
  review:
    summary: Mitochondrial localization is correct but less specific than the established inner-membrane localization.
    action: MODIFY
    reason: The earliest localization work supports mitochondria, and later biochemical/structural work resolves AFG3L2 to the mitochondrial inner membrane.
    proposed_replacement_terms:
    - id: GO:0005743
      label: mitochondrial inner membrane
    supported_by:
    - reference_id: PMID:10395799
      supporting_text: Immunofluorescence studies revealed that AFG3L2 and paraplegin share a similar expression pattern and the same subcellular localization, the mitochondrial compartment.
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0141164
    label: mitochondrial protein quality control
  evidence_type: IDA
  original_reference_id: PMID:26504172
  qualifier: involved_in
  review:
    summary: AFG3L2 performs mitochondrial protein quality control, especially for newly synthesized or misassembled inner-membrane proteins.
    action: ACCEPT
    reason: This is a core process annotation supported by direct perturbation and mitochondrial translation/proteostasis studies.
    supported_by:
    - reference_id: PMID:26504172
      supporting_text: The mitochondrial m-AAA protease subunit AFG3L2 is critical to this surveillance mechanism
    - reference_id: PMID:30683687
      supporting_text: Responsive quality control mechanisms are needed to ensure that aberrant protein synthesis does not disrupt mitochondrial function.
    - reference_id: PMID:34718584
      supporting_text: defects in the OXA1L-mediated insertion of MT-ATP6 nascent chains into the mitochondrial inner membrane are rapidly resolved by the AFG3L2 protease complex
    - reference_id: file:human/AFG3L2/AFG3L2-deep-research-falcon.md
      supporting_text: '**m-AAA proteases** are IMM-embedded ATP-dependent protease complexes that provide **protein quality control (PQC)** by selective removal/processing of **non-assembled** or **damaged** mitochondrial proteins'
- term:
    id: GO:0141164
    label: mitochondrial protein quality control
  evidence_type: IDA
  original_reference_id: PMID:30683687
  qualifier: involved_in
  review:
    summary: AFG3L2 performs mitochondrial protein quality control, especially for newly synthesized or misassembled inner-membrane proteins.
    action: ACCEPT
    reason: This is a core process annotation supported by direct perturbation and mitochondrial translation/proteostasis studies.
    supported_by:
    - reference_id: PMID:26504172
      supporting_text: The mitochondrial m-AAA protease subunit AFG3L2 is critical to this surveillance mechanism
    - reference_id: PMID:30683687
      supporting_text: Responsive quality control mechanisms are needed to ensure that aberrant protein synthesis does not disrupt mitochondrial function.
    - reference_id: PMID:34718584
      supporting_text: defects in the OXA1L-mediated insertion of MT-ATP6 nascent chains into the mitochondrial inner membrane are rapidly resolved by the AFG3L2 protease complex
- term:
    id: GO:0141164
    label: mitochondrial protein quality control
  evidence_type: IDA
  original_reference_id: PMID:34718584
  qualifier: involved_in
  review:
    summary: AFG3L2 performs mitochondrial protein quality control, especially for newly synthesized or misassembled inner-membrane proteins.
    action: ACCEPT
    reason: This is a core process annotation supported by direct perturbation and mitochondrial translation/proteostasis studies.
    supported_by:
    - reference_id: PMID:26504172
      supporting_text: The mitochondrial m-AAA protease subunit AFG3L2 is critical to this surveillance mechanism
    - reference_id: PMID:30683687
      supporting_text: Responsive quality control mechanisms are needed to ensure that aberrant protein synthesis does not disrupt mitochondrial function.
    - reference_id: PMID:34718584
      supporting_text: defects in the OXA1L-mediated insertion of MT-ATP6 nascent chains into the mitochondrial inner membrane are rapidly resolved by the AFG3L2 protease complex
- term:
    id: GO:0004222
    label: metalloendopeptidase activity
  evidence_type: IDA
  original_reference_id: PMID:29545505
  qualifier: enables
  review:
    summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit.
    action: ACCEPT
    reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
- term:
    id: GO:0004222
    label: metalloendopeptidase activity
  evidence_type: IDA
  original_reference_id: PMID:27642048
  qualifier: enables
  review:
    summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit.
    action: ACCEPT
    reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
- term:
    id: GO:0004222
    label: metalloendopeptidase activity
  evidence_type: IDA
  original_reference_id: PMID:28396416
  qualifier: enables
  review:
    summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit.
    action: ACCEPT
    reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: IDA
  original_reference_id: PMID:37917749
  qualifier: is_active_in
  review:
    summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side.
    action: ACCEPT
    reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0005745
    label: m-AAA complex
  evidence_type: IDA
  original_reference_id: PMID:28396416
  qualifier: part_of
  review:
    summary: AFG3L2 is a constituent of the mitochondrial m-AAA protease complex, as homohexamers and as heterohexamers with SPG7.
    action: ACCEPT
    reason: The m-AAA complex is the correct cellular component context for AFG3L2 protease function.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7)
    - reference_id: PMID:14623864
      supporting_text: paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane
- term:
    id: GO:0110097
    label: regulation of calcium import into the mitochondrion
  evidence_type: IDA
  original_reference_id: PMID:27642048
  qualifier: involved_in
  review:
    summary: AFG3L2 regulates mitochondrial calcium import by degrading unassembled EMRE before MCU complex assembly.
    action: KEEP_AS_NON_CORE
    reason: This is a supported substrate-specific consequence of m-AAA proteolysis, but not the central gene-level function.
    supported_by:
    - reference_id: PMID:27642048
      supporting_text: the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU
    - reference_id: PMID:28396416
      supporting_text: mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis
- term:
    id: GO:0110097
    label: regulation of calcium import into the mitochondrion
  evidence_type: IDA
  original_reference_id: PMID:28396416
  qualifier: involved_in
  review:
    summary: AFG3L2 regulates mitochondrial calcium import by degrading unassembled EMRE before MCU complex assembly.
    action: KEEP_AS_NON_CORE
    reason: This is a supported substrate-specific consequence of m-AAA proteolysis, but not the central gene-level function.
    supported_by:
    - reference_id: PMID:27642048
      supporting_text: the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU
    - reference_id: PMID:28396416
      supporting_text: mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis
- term:
    id: GO:0004222
    label: metalloendopeptidase activity
  evidence_type: IDA
  original_reference_id: PMID:37917749
  qualifier: enables
  review:
    summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit.
    action: ACCEPT
    reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
- term:
    id: GO:0004222
    label: metalloendopeptidase activity
  evidence_type: IDA
  original_reference_id: PMID:38157846
  qualifier: enables
  review:
    summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit.
    action: ACCEPT
    reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: PMID:31327635
  qualifier: is_active_in
  review:
    summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side.
    action: ACCEPT
    reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0030163
    label: protein catabolic process
  evidence_type: IDA
  original_reference_id: PMID:37917749
  qualifier: involved_in
  review:
    summary: Protein catabolic process is correct but too broad for the directly supported mitochondrial degradation role.
    action: MODIFY
    reason: AFG3L2 degrades mitochondrial inner membrane and matrix-facing substrates; the PN projection to mitochondrial protein catabolic process is conservative and literature-supported.
    proposed_replacement_terms:
    - id: GO:0035694
      label: mitochondrial protein catabolic process
    supported_by:
    - reference_id: PMID:37917749
      supporting_text: Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2.
    - reference_id: PMID:38157846
      supporting_text: mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1
    - reference_id: file:projects/PROTEOSTASIS/reports/pn_projection/pn_projected_annotations.tsv
      supporting_text: This PN class groups mitochondrial protein-degradation pathways. GO mitochondrial protein catabolic process is the conservative shared target.
- term:
    id: GO:0030163
    label: protein catabolic process
  evidence_type: IDA
  original_reference_id: PMID:38157846
  qualifier: involved_in
  review:
    summary: Protein catabolic process is correct but too broad for the directly supported mitochondrial degradation role.
    action: MODIFY
    reason: AFG3L2 degrades mitochondrial inner membrane and matrix-facing substrates; the PN projection to mitochondrial protein catabolic process is conservative and literature-supported.
    proposed_replacement_terms:
    - id: GO:0035694
      label: mitochondrial protein catabolic process
    supported_by:
    - reference_id: PMID:37917749
      supporting_text: Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2.
    - reference_id: PMID:38157846
      supporting_text: mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1
    - reference_id: file:projects/PROTEOSTASIS/reports/pn_projection/pn_projected_annotations.tsv
      supporting_text: This PN class groups mitochondrial protein-degradation pathways. GO mitochondrial protein catabolic process is the conservative shared target.
- term:
    id: GO:0072753
    label: cellular response to glutathione
  evidence_type: IDA
  original_reference_id: PMID:37917749
  qualifier: involved_in
  review:
    summary: AFG3L2 participates in the glutathione-response circuit by degrading SLC25A39 when mitochondrial glutathione is sufficient.
    action: KEEP_AS_NON_CORE
    reason: The annotation reflects a specific regulatory substrate and metabolite-feedback axis, but the core function remains mitochondrial proteolysis.
    supported_by:
    - reference_id: PMID:37917749
      supporting_text: Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2.
    - reference_id: PMID:38157846
      supporting_text: mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1
- term:
    id: GO:0072753
    label: cellular response to glutathione
  evidence_type: IDA
  original_reference_id: PMID:38157846
  qualifier: involved_in
  review:
    summary: AFG3L2 participates in the glutathione-response circuit by degrading SLC25A39 when mitochondrial glutathione is sufficient.
    action: KEEP_AS_NON_CORE
    reason: The annotation reflects a specific regulatory substrate and metabolite-feedback axis, but the core function remains mitochondrial proteolysis.
    supported_by:
    - reference_id: PMID:37917749
      supporting_text: Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2.
    - reference_id: PMID:38157846
      supporting_text: mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1
- term:
    id: GO:0004222
    label: metalloendopeptidase activity
  evidence_type: IDA
  original_reference_id: PMID:19748354
  qualifier: enables
  review:
    summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit.
    action: ACCEPT
    reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
- term:
    id: GO:0004222
    label: metalloendopeptidase activity
  evidence_type: IDA
  original_reference_id: PMID:29932645
  qualifier: enables
  review:
    summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit.
    action: ACCEPT
    reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
- term:
    id: GO:0004222
    label: metalloendopeptidase activity
  evidence_type: IDA
  original_reference_id: PMID:31327635
  qualifier: enables
  review:
    summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit.
    action: ACCEPT
    reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
- term:
    id: GO:0005745
    label: m-AAA complex
  evidence_type: IDA
  original_reference_id: PMID:19748354
  qualifier: part_of
  review:
    summary: AFG3L2 is a constituent of the mitochondrial m-AAA protease complex, as homohexamers and as heterohexamers with SPG7.
    action: ACCEPT
    reason: The m-AAA complex is the correct cellular component context for AFG3L2 protease function.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7)
    - reference_id: PMID:14623864
      supporting_text: paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane
- term:
    id: GO:0005745
    label: m-AAA complex
  evidence_type: IDA
  original_reference_id: PMID:31327635
  qualifier: part_of
  review:
    summary: AFG3L2 is a constituent of the mitochondrial m-AAA protease complex, as homohexamers and as heterohexamers with SPG7.
    action: ACCEPT
    reason: The m-AAA complex is the correct cellular component context for AFG3L2 protease function.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7)
    - reference_id: PMID:14623864
      supporting_text: paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane
- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IDA
  original_reference_id: PMID:19748354
  qualifier: enables
  review:
    summary: ATP hydrolysis is a core motor activity of the AAA+ ring that powers substrate unfolding and translocation.
    action: ACCEPT
    reason: This is directly supported by m-AAA ATPase assays and AFG3L2 structural work tying ATP-dependent translocation to substrate degradation.
    supported_by:
    - reference_id: PMID:19748354
      supporting_text: we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes
    - reference_id: PMID:31327635
      supporting_text: ATP-dependent translocation to unfold and degrade targeted proteins
- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IDA
  original_reference_id: PMID:31327635
  qualifier: enables
  review:
    summary: ATP hydrolysis is a core motor activity of the AAA+ ring that powers substrate unfolding and translocation.
    action: ACCEPT
    reason: This is directly supported by m-AAA ATPase assays and AFG3L2 structural work tying ATP-dependent translocation to substrate degradation.
    supported_by:
    - reference_id: PMID:19748354
      supporting_text: we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes
    - reference_id: PMID:31327635
      supporting_text: ATP-dependent translocation to unfold and degrade targeted proteins
- term:
    id: GO:0051604
    label: protein maturation
  evidence_type: IDA
  original_reference_id: PMID:29932645
  qualifier: involved_in
  review:
    summary: Protein maturation is true for selected substrates but too generic.
    action: MODIFY
    reason: The evidence points to mitochondrial protein processing/maturation, especially MRPL32 and related mitochondrial substrates.
    proposed_replacement_terms:
    - id: GO:0034982
      label: mitochondrial protein processing
    supported_by:
    - reference_id: PMID:29932645
      supporting_text: conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form
    - reference_id: PMID:41075794
      supporting_text: SLC25A45-FLAG levels only increased in cells treated with siRNA targeting AFG3L2
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:35912435
  qualifier: enables
  supporting_entities:
  - UniProtKB:Q9H3K2
  review:
    summary: The IPI row records binding to UniProtKB:Q9H3K2, but protein binding is too generic to describe AFG3L2 function.
    action: MARK_AS_OVER_ANNOTATED
    reason: Specific interactions should be interpreted through m-AAA complex membership, substrate degradation, calcium regulation, or other informative process terms rather than the generic protein binding MF term.
    supported_by:
    - reference_id: PMID:35912435
      supporting_text: Besides these expected interactors, TMBIM5 (also known as GHITM or MICS1) was highly enriched in AFG3L2 precipitates
- term:
    id: GO:0006508
    label: proteolysis
  evidence_type: IDA
  original_reference_id: PMID:35912435
  qualifier: involved_in
  review:
    summary: Generic proteolysis is correct but underspecified for the mitochondrial m-AAA protease role.
    action: MODIFY
    reason: The evidence supports mitochondrial substrate degradation and protein quality control, not merely generic proteolysis.
    proposed_replacement_terms:
    - id: GO:0035694
      label: mitochondrial protein catabolic process
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
    - reference_id: file:projects/PROTEOSTASIS/reports/pn_projection/pn_projected_annotations.tsv
      supporting_text: This PN class groups mitochondrial protein-degradation pathways. GO mitochondrial protein catabolic process is the conservative shared target.
- term:
    id: GO:0004222
    label: metalloendopeptidase activity
  evidence_type: IDA
  original_reference_id: PMID:22354088
  qualifier: enables
  review:
    summary: Metalloendopeptidase activity is the core catalytic activity of AFG3L2 as an m-AAA protease subunit.
    action: ACCEPT
    reason: Direct structural and biochemical studies support AFG3L2 as a zinc metalloprotease that cleaves substrates after ATP-driven translocation.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IDA
  original_reference_id: PMID:22354088
  qualifier: located_in
  review:
    summary: Mitochondrial localization is correct but less specific than the established inner-membrane localization.
    action: MODIFY
    reason: The earliest localization work supports mitochondria, and later biochemical/structural work resolves AFG3L2 to the mitochondrial inner membrane.
    proposed_replacement_terms:
    - id: GO:0005743
      label: mitochondrial inner membrane
    supported_by:
    - reference_id: PMID:10395799
      supporting_text: Immunofluorescence studies revealed that AFG3L2 and paraplegin share a similar expression pattern and the same subcellular localization, the mitochondrial compartment.
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0033619
    label: membrane protein proteolysis
  evidence_type: IDA
  original_reference_id: PMID:22354088
  qualifier: involved_in
  review:
    summary: AFG3L2 participates in proteolysis of mitochondrial membrane-associated proteins such as PINK1 and inner-membrane substrates.
    action: ACCEPT
    reason: The term is consistent with direct m-AAA substrate degradation, although the added mitochondrial protein catabolic process term captures the broader mitochondrial context.
    supported_by:
    - reference_id: PMID:22354088
      supporting_text: we identified four mitochondrial proteases, mitochondrial processing peptidase (MPP), presenilin-associated rhomboid-like protease (PARL), m-AAA and ClpXP, involved in PINK1 degradation
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:26387735
  qualifier: enables
  supporting_entities:
  - UniProtKB:Q9UQ90
  review:
    summary: The IPI row records binding to UniProtKB:Q9UQ90, but protein binding is too generic to describe AFG3L2 function.
    action: MARK_AS_OVER_ANNOTATED
    reason: Specific interactions should be interpreted through m-AAA complex membership, substrate degradation, calcium regulation, or other informative process terms rather than the generic protein binding MF term.
    supported_by:
    - reference_id: PMID:14623864
      supporting_text: To explore a potential physical interaction between paraplegin and AFG3L2, we performed coimmunoprecipitation studies in HEK293.
    - reference_id: PMID:26387735
      supporting_text: HA antibody immunoprecipitated a known SPG7 binding partner AFG3L2
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: located_in
  supporting_entities:
  - UniProtKB:Q8JZQ2
  review:
    summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side.
    action: ACCEPT
    reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0016485
    label: protein processing
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  supporting_entities:
  - UniProtKB:Q8JZQ2
  review:
    summary: Protein processing is true but should be represented with the existing mitochondrial protein processing term.
    action: MODIFY
    reason: AFG3L2 processing events occur in mitochondria and are already captured more specifically by mitochondrial protein processing.
    proposed_replacement_terms:
    - id: GO:0034982
      label: mitochondrial protein processing
    supported_by:
    - reference_id: PMID:29932645
      supporting_text: conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form
    - reference_id: PMID:41075794
      supporting_text: SLC25A45-FLAG levels only increased in cells treated with siRNA targeting AFG3L2
- term:
    id: GO:0016540
    label: protein autoprocessing
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  supporting_entities:
  - UniProtKB:Q8JZQ2
  review:
    summary: Autoprocessing of the imported precursor is described for AFG3L2, but it is ancillary to the mature protease role.
    action: KEEP_AS_NON_CORE
    reason: Retain as non-core because the main biological function is degradation/processing of mitochondrial substrates.
    supported_by:
    - reference_id: file:human/AFG3L2/AFG3L2-uniprot.txt
      supporting_text: autocatalytic proteolytic processing to generate the proteolytically active mature form
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-8949649
  qualifier: located_in
  review:
    summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side.
    action: ACCEPT
    reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-8949659
  qualifier: located_in
  review:
    summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side.
    action: ACCEPT
    reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-8949661
  qualifier: located_in
  review:
    summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side.
    action: ACCEPT
    reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9838627
  qualifier: located_in
  review:
    summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side.
    action: ACCEPT
    reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9839053
  qualifier: located_in
  review:
    summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side.
    action: ACCEPT
    reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9839059
  qualifier: located_in
  review:
    summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side.
    action: ACCEPT
    reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9839105
  qualifier: located_in
  review:
    summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side.
    action: ACCEPT
    reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9839113
  qualifier: located_in
  review:
    summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side.
    action: ACCEPT
    reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9839149
  qualifier: located_in
  review:
    summary: AFG3L2 is an integral mitochondrial inner membrane protein with catalytic domains exposed to the matrix side.
    action: ACCEPT
    reason: This is the most specific and best-supported cellular component annotation. Matrix-facing catalytic topology does not make the protein a soluble mitochondrial matrix component.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:27642048
  qualifier: enables
  supporting_entities:
  - UniProtKB:Q8WWC4
  review:
    summary: The IPI row records binding to UniProtKB:Q8WWC4, but protein binding is too generic to describe AFG3L2 function.
    action: MARK_AS_OVER_ANNOTATED
    reason: Specific interactions should be interpreted through m-AAA complex membership, substrate degradation, calcium regulation, or other informative process terms rather than the generic protein binding MF term.
    supported_by:
    - reference_id: PMID:27642048
      supporting_text: MAIP1 assists biogenesis of the MCU subunit EMRE, the m-AAA protease degrades non-assembled EMRE
    - reference_id: PMID:27642048
      supporting_text: the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:27642048
  qualifier: enables
  supporting_entities:
  - UniProtKB:Q9H4I9
  review:
    summary: The IPI row records binding to UniProtKB:Q9H4I9, but protein binding is too generic to describe AFG3L2 function.
    action: MARK_AS_OVER_ANNOTATED
    reason: Specific interactions should be interpreted through m-AAA complex membership, substrate degradation, calcium regulation, or other informative process terms rather than the generic protein binding MF term.
    supported_by:
    - reference_id: PMID:27642048
      supporting_text: MAIP1 assists biogenesis of the MCU subunit EMRE, the m-AAA protease degrades non-assembled EMRE
    - reference_id: PMID:27642048
      supporting_text: the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU
- term:
    id: GO:0006508
    label: proteolysis
  evidence_type: IMP
  original_reference_id: PMID:27642048
  qualifier: involved_in
  review:
    summary: Generic proteolysis is correct but underspecified for the mitochondrial m-AAA protease role.
    action: MODIFY
    reason: The evidence supports mitochondrial substrate degradation and protein quality control, not merely generic proteolysis.
    proposed_replacement_terms:
    - id: GO:0035694
      label: mitochondrial protein catabolic process
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
    - reference_id: file:projects/PROTEOSTASIS/reports/pn_projection/pn_projected_annotations.tsv
      supporting_text: This PN class groups mitochondrial protein-degradation pathways. GO mitochondrial protein catabolic process is the conservative shared target.
- term:
    id: GO:0007409
    label: axonogenesis
  evidence_type: IMP
  original_reference_id: PMID:27642048
  qualifier: involved_in
  review:
    summary: Axonogenesis reflects a neuronal phenotype of impaired m-AAA protease function rather than a direct molecular role.
    action: KEEP_AS_NON_CORE
    reason: Retain as non-core/developmental consequence; do not use it to define AFG3L2 core function.
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: m-AAA proteases are essential for axonal development in mammals
    - reference_id: PMID:27642048
      supporting_text: Loss of the m-AAA protease results in accumulation of constitutively active MCU-EMRE channels
- term:
    id: GO:0008237
    label: metallopeptidase activity
  evidence_type: IMP
  original_reference_id: PMID:27642048
  qualifier: enables
  review:
    summary: The annotation is directionally correct but too broad for AFG3L2.
    action: MODIFY
    reason: AFG3L2 is specifically supported as a metalloendopeptidase/m-AAA protease; use the more precise metalloendopeptidase activity term.
    proposed_replacement_terms:
    - id: GO:0004222
      label: metalloendopeptidase activity
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
- term:
    id: GO:0036444
    label: calcium import into the mitochondrion
  evidence_type: IMP
  original_reference_id: PMID:27642048
  qualifier: involved_in
  review:
    summary: The calcium-import phenotype is mediated through regulation of EMRE/MCU assembly rather than direct calcium transport by AFG3L2.
    action: MODIFY
    reason: Use regulation of calcium import into the mitochondrion rather than annotating AFG3L2 as directly involved in calcium import.
    proposed_replacement_terms:
    - id: GO:0110097
      label: regulation of calcium import into the mitochondrion
    supported_by:
    - reference_id: PMID:27642048
      supporting_text: the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU
    - reference_id: PMID:28396416
      supporting_text: mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis
- term:
    id: GO:0051560
    label: mitochondrial calcium ion homeostasis
  evidence_type: IMP
  original_reference_id: PMID:27642048
  qualifier: involved_in
  review:
    summary: AFG3L2 contributes to mitochondrial calcium homeostasis through EMRE turnover and MCU gatekeeper assembly.
    action: KEEP_AS_NON_CORE
    reason: Supported but downstream/substrate-specific relative to the m-AAA protease quality-control function.
    supported_by:
    - reference_id: PMID:27642048
      supporting_text: the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU
    - reference_id: PMID:28396416
      supporting_text: mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:14623864
  qualifier: enables
  supporting_entities:
  - UniProtKB:Q9UQ90
  review:
    summary: The IPI row records binding to UniProtKB:Q9UQ90, but protein binding is too generic to describe AFG3L2 function.
    action: MARK_AS_OVER_ANNOTATED
    reason: Specific interactions should be interpreted through m-AAA complex membership, substrate degradation, calcium regulation, or other informative process terms rather than the generic protein binding MF term.
    supported_by:
    - reference_id: PMID:14623864
      supporting_text: To explore a potential physical interaction between paraplegin and AFG3L2, we performed coimmunoprecipitation studies in HEK293.
    - reference_id: PMID:26387735
      supporting_text: HA antibody immunoprecipitated a known SPG7 binding partner AFG3L2
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: TAS
  original_reference_id: PMID:10395799
  qualifier: located_in
  review:
    summary: Mitochondrial localization is correct but less specific than the established inner-membrane localization.
    action: MODIFY
    reason: The earliest localization work supports mitochondria, and later biochemical/structural work resolves AFG3L2 to the mitochondrial inner membrane.
    proposed_replacement_terms:
    - id: GO:0005743
      label: mitochondrial inner membrane
    supported_by:
    - reference_id: PMID:10395799
      supporting_text: Immunofluorescence studies revealed that AFG3L2 and paraplegin share a similar expression pattern and the same subcellular localization, the mitochondrial compartment.
    - reference_id: PMID:31327635
      supporting_text: m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively
    - reference_id: PMID:14623864
      supporting_text: Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane
- term:
    id: GO:0035694
    label: mitochondrial protein catabolic process
  evidence_type: IC
  original_reference_id: PMID:31327635
  qualifier: involved_in
  review:
    summary: Proposed new annotation from the Proteostasis Network projection. AFG3L2 directly degrades mitochondrial substrates as an inner-membrane m-AAA protease, so mitochondrial protein catabolic process is a conservative addition.
    action: NEW
    reason: The PN projection flagged GO:0035694 as more specific than the existing generic protein catabolic process annotation. Literature supports mitochondrial substrate degradation, while the parallel PN matrix localization projection is not accepted because AFG3L2 is an inner membrane protein with matrix-facing catalytic domains.
    additional_reference_ids:
    - file:human/AFG3L2/AFG3L2-notes.md
    - file:human/AFG3L2/AFG3L2-deep-research-falcon.md
    supported_by:
    - reference_id: PMID:31327635
      supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
    - reference_id: PMID:29932645
      supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
    - reference_id: PMID:37917749
      supporting_text: Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2.
    - reference_id: file:projects/PROTEOSTASIS/reports/pn_projection/pn_projected_annotations.tsv
      supporting_text: This PN class groups mitochondrial protein-degradation pathways. GO mitochondrial protein catabolic process is the conservative shared target.
    - reference_id: file:human/AFG3L2/AFG3L2-deep-research-falcon.md
      supporting_text: '**m-AAA proteases** are IMM-embedded ATP-dependent protease complexes that provide **protein quality control (PQC)** by selective removal/processing of **non-assembled** or **damaged** mitochondrial proteins'
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000052
  title: Gene Ontology annotation based on curation of immunofluorescence data
  findings: []
- id: GO_REF:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:10395799
  title: Identification and characterization of AFG3L2, a novel paraplegin-related gene.
  findings: []
- id: PMID:14623864
  title: Loss of m-AAA protease in mitochondria causes complex I deficiency and increased sensitivity to oxidative stress in hereditary spastic paraplegia.
  findings: []
- id: PMID:19748354
  title: An intersubunit signaling network coordinates ATP hydrolysis by m-AAA proteases.
  findings: []
- id: PMID:22354088
  title: Mitochondrial processing peptidase regulates PINK1 processing, import and Parkin recruitment.
  findings: []
- id: PMID:26387735
  title: SPG7 Is an Essential and Conserved Component of the Mitochondrial Permeability Transition Pore.
  findings: []
- id: PMID:26504172
  title: Quality control of mitochondrial protein synthesis is required for membrane integrity and cell fitness.
  findings: []
- id: PMID:27642048
  title: The m-AAA Protease Associated with Neurodegeneration Limits MCU Activity in Mitochondria.
  findings: []
- id: PMID:28396416
  title: Proteolytic control of the mitochondrial calcium uniporter complex.
  findings: []
- id: PMID:29545505
  title: m-AAA and i-AAA complexes coordinate to regulate OMA1, the stress-activated supervisor of mitochondrial dynamics.
  findings: []
- id: PMID:29932645
  title: Dissecting Substrate Specificities of the Mitochondrial AFG3L2 Protease.
  findings: []
- id: PMID:30683687
  title: Mitochondrial stress response triggered by defects in protein synthesis quality control.
  findings: []
- id: PMID:31327635
  title: Unique Structural Features of the Mitochondrial AAA+ Protease AFG3L2 Reveal the Molecular Basis for Activity in Health and Disease.
  findings: []
- id: PMID:32814053
  title: Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
  findings: []
- id: PMID:34718584
  title: Translation of MT-ATP6 pathogenic variants reveals distinct regulatory consequences from the co-translational quality control of mitochondrial protein synthesis.
  findings: []
- id: PMID:34800366
  title: Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context.
  findings: []
- id: PMID:35912435
  title: Regulation of mitochondrial proteostasis by the proton gradient.
  findings: []
- id: PMID:37917749
  title: Autoregulatory control of mitochondrial glutathione homeostasis.
  findings: []
- id: PMID:38157846
  title: Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis.
  findings: []
- id: PMID:41075794
  title: SLC25A45 is required for mitochondrial uptake of methylated amino acids and de novo carnitine biosynthesis.
  findings: []
- id: Reactome:R-HSA-8949649
  title: PMPCA:PMPCB cleaves the transit peptide of proSMDT1 (proEMRE)
  findings: []
- id: Reactome:R-HSA-8949659
  title: AFG3L2 (m-AAA protease) degrades SMDT1 that is not assembled in MCU
  findings: []
- id: Reactome:R-HSA-8949661
  title: C2orf47:AFG3L2 binds the transit peptide of SMDT1
  findings: []
- id: Reactome:R-HSA-9838627
  title: AFG3L2 binds mitochondrial inner membrane proteins
  findings: []
- id: Reactome:R-HSA-9839053
  title: AFG3L2:SPG7 binds SMDT1 (EMRE)
  findings: []
- id: Reactome:R-HSA-9839059
  title: AFG3L2:SPG7 degrades SMDT1 (EMRE)
  findings: []
- id: Reactome:R-HSA-9839105
  title: AFG3L2 degrades mitochondrial matrix proteins
  findings: []
- id: Reactome:R-HSA-9839113
  title: AFG3L2 degrades mitochondrial inner membrane proteins
  findings: []
- id: Reactome:R-HSA-9839149
  title: AFG3L2 binds mitochondrial matrix proteins
  findings: []
- id: file:human/AFG3L2/AFG3L2-uniprot.txt
  title: UniProtKB record for human AFG3L2 (Q9Y4W6)
  findings: []
- id: file:human/AFG3L2/AFG3L2-deep-research-falcon.md
  title: Falcon deep research report for human AFG3L2
  findings: []
- id: file:human/AFG3L2/AFG3L2-notes.md
  title: AFG3L2 curator notes for Proteostasis PN review
  findings: []
- id: file:projects/PROTEOSTASIS/reports/pn_projection/pn_projected_annotations.tsv
  title: Proteostasis Network projected GO annotations report
  findings: []
- id: file:projects/PROTEOSTASIS/mappings/mitochondrial_proteostasis.yaml
  title: Proteostasis Network mitochondrial proteostasis mapping
  findings: []
core_functions:
- description: ATP-dependent zinc metalloendopeptidase activity in the mitochondrial m-AAA protease. AFG3L2 uses its AAA+ motor to engage and unfold mitochondrial substrates and its M41 protease active sites to cleave them, supporting mitochondrial protein catabolic process, mitochondrial protein processing, and mitochondrial protein quality control.
  molecular_function:
    id: GO:0004222
    label: metalloendopeptidase activity
  directly_involved_in:
  - id: GO:0035694
    label: mitochondrial protein catabolic process
  - id: GO:0034982
    label: mitochondrial protein processing
  - id: GO:0141164
    label: mitochondrial protein quality control
  locations:
  - id: GO:0005743
    label: mitochondrial inner membrane
  in_complex:
    id: GO:0005745
    label: m-AAA complex
  supported_by:
  - reference_id: PMID:31327635
    supporting_text: structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins
  - reference_id: PMID:29932645
    supporting_text: Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane.
  - reference_id: PMID:26504172
    supporting_text: The mitochondrial m-AAA protease subunit AFG3L2 is critical to this surveillance mechanism
  - reference_id: PMID:29932645
    supporting_text: conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form
- description: AAA+ ATP hydrolysis that powers substrate unfolding, membrane-proximal engagement, and translocation into the proteolytic chamber of the m-AAA complex.
  molecular_function:
    id: GO:0016887
    label: ATP hydrolysis activity
  directly_involved_in:
  - id: GO:0035694
    label: mitochondrial protein catabolic process
  locations:
  - id: GO:0005743
    label: mitochondrial inner membrane
  in_complex:
    id: GO:0005745
    label: m-AAA complex
  supported_by:
  - reference_id: PMID:19748354
    supporting_text: we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes
  - reference_id: PMID:31327635
    supporting_text: ATP-dependent translocation to unfold and degrade targeted proteins
proposed_new_terms: []
suggested_questions:
- question: Should matrix-facing but inner-membrane-anchored m-AAA proteases such as AFG3L2 be represented only with mitochondrial inner membrane/is_active_in annotations, or should GO curation add an annotation extension indicating that the catalytic domain faces the matrix?
  experts:
  - Puchades C
  - Glynn SE
  - Langer T
- question: For AFG3L2 substrates such as SLC25A39 and SLC25A45, should curators represent metabolite-homeostasis consequences as non-core process annotations or restrict gene-level annotations to the proteolytic event and mitochondrial protein catabolic process?
  experts:
  - Birsoy K
  - Shen H
  - MacVicar T
suggested_experiments:
- hypothesis: AFG3L2 substrates can be prioritized by matrix-exposed degrons and metabolite-sensitive conformational states rather than by generic inner-membrane localization alone.
  description: Combine pulse-chase proteomics in AFG3L2 knockout/rescue cells with degron-mutant substrate panels for SLC25A39, SLC25A45, EMRE, and TMBIM5, measuring substrate half-life, AFG3L2 association, and mitochondrial metabolite or calcium readouts.
  experiment_type: proteomics and targeted substrate-turnover assays

AFG3L2

Gene Description

Existing Annotations Review

Core Functions

AAA+ ATP hydrolysis that powers substrate unfolding, membrane-proximal engagement, and translocation into the proteolytic chamber of the m-AAA complex.

References

Suggested Questions for Experts

Suggested Experiments

Deep Research

Falcon

Comprehensive Research Report: Human AFG3L2 (UniProt Q9Y4W6) — Functional Annotation and Disease Relevance

Executive summary

1) Gene/protein identity verification (mandatory)

2) Key concepts and definitions (current understanding)

2.1 m-AAA protease and mitochondrial proteostasis

2.2 Domain logic and catalytic mechanism (AAA+ ATPase + Zn metalloprotease)

2.3 Subcellular localization and topology

3) Primary molecular function: reaction, substrate specificity, and pathways

3.1 Primary biochemical function

3.2 Experimentally supported substrates (high-confidence examples)

3.2.1 SLC25A39 (mitochondrial glutathione transporter) — metabolic feedback control (2023)

3.2.2 MRPL32 / bL32m (mitoribosome biogenesis)

3.2.3 EMRE (MCU regulator) — mitochondrial Ca2+ handling

3.2.4 TIMMDC1 (Complex I assembly factor)

3.2.5 TMBIM5/GHITM (Ca2+/H+ homeostasis; inhibitor-substrate duality)

3.2.6 Expanded substrate landscape in hypoxia: RNA metabolism and biogenesis factors (2024)

4) Recent developments and latest research (prioritize 2023–2024)

4.1 2023: AFG3L2 couples glutathione availability to transporter turnover

4.2 2024: Disease mechanism and therapy concept in SPAX5 — ISR as protective output

4.3 2024: Hypoxia signaling connects AFG3L2 to control of mitochondrial biogenesis and gene expression

5) Current applications and real-world implementations

5.1 Clinical genetics and diagnostics

5.2 Preclinical therapeutic strategies with translational logic

5.3 Biomarkers and mechanistic readouts

6) Human phenotypes and genotype–phenotype mapping (current 2024 view)

6.1 Dominant SCA28 (MIM#610246)

6.2 Dominant optic neuropathy: DOA12/OPA12 (MIM#618977)

6.3 Recessive early-onset spastic ataxia-neuropathy: SPAX5 / spastic ataxia type 5

7) Expert opinion / analysis (authoritative perspectives grounded in evidence)

8) Relevant statistics and quantitative data (from recent studies)

9) Evidence map (structured summary)

10) Limitations of the current evidence base (important for annotation quality)

Key recent sources (URLs + publication timing)

Artifacts

Citations

📚 Additional Documentation

Notes

AFG3L2 notes

2026-06-03 Proteostasis PN review

Literature synthesis

PN projection evaluation

Annotation strategy

Pn Notes

AFG3L2 PN Consistency Notes

Source Files Checked

Deep Research Files

AIGR Review Snapshot

PN Consistency Summary

Full Consistency Review

PN Dossier Context

PN row 1: Mitochondrial proteostasis | Organelle-specific protein degradation | Matrix protease

Projected GO annotations (2)

Note

📄 View Raw YAML