Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005739 mitochondrion	IBA GO_REF:0000033	ACCEPT	Summary: ISCA2 is confirmed to localize to mitochondria based on phylogenetic inference (IBA) and multiple experimental studies. The protein functions in the mitochondrial matrix as part of the late-stage ISC assembly pathway (PMID:22323289, PMID:25347204). Reason: Mitochondrial localization is well-established for ISCA2. The IBA annotation is consistent with experimental evidence showing ISCA2 functions in mitochondrial [4Fe-4S] cluster assembly. Direct experimental evidence (IDA from PMID:22323289) also confirms this localization. Supporting Evidence: PMID:25347204 The generation of [4Fe-4S] clusters in mitochondria critically depends, in both yeast and human cells, on two A-type ISC proteins (in mammals named ISCA1 and ISCA2)
GO:0016226 iron-sulfur cluster assembly	IBA GO_REF:0000033	ACCEPT	Summary: ISCA2 is directly involved in iron-sulfur cluster assembly, specifically in the late-stage [4Fe-4S] cluster assembly pathway. The IBA annotation appropriately captures this core function (PMID:25347204). Reason: While ISCA2's role is specifically in [4Fe-4S] cluster assembly, the general term iron-sulfur cluster assembly is still correct and appropriate. The ISCA1:ISCA2 heterodimeric complex receives [2Fe-2S] clusters from GRX5 and assembles them into [4Fe-4S] clusters (PMID:25347204). The IBA annotation from PANTHER is valid. Supporting Evidence: PMID:25347204 The generation of [4Fe-4S] clusters in mitochondria critically depends, in both yeast and human cells, on two A-type ISC proteins (in mammals named ISCA1 and ISCA2) file:human/ISCA2/ISCA2-deep-research-falcon.md ISCA2 is a mitochondrial A-type Fe-S assembly factor in the HesB/IscA family. It acts as a late-acting secondary carrier in the ISC pathway
GO:0051604 protein maturation	IBA GO_REF:0000033	ACCEPT	Summary: ISCA2 contributes to the maturation of mitochondrial [4Fe-4S] proteins by facilitating the assembly and transfer of [4Fe-4S] clusters to apo-proteins including aconitase and lipoic acid synthase (PMID:22323289, PMID:25347204). Reason: This annotation correctly captures ISCA2's role in promoting the maturation of [4Fe-4S]-containing proteins. The term is appropriate as ISCA2 is required for the functional maturation of mitochondrial [4Fe-4S] proteins. Supporting Evidence: PMID:25347204 These findings imply that such heterodimeric complex is the functional unit in mitochondria receiving [2Fe-2S] clusters from hGRX5 and assembling [4Fe-4S] clusters before their transfer to the final target apo proteins
GO:0005506 iron ion binding	IBA GO_REF:0000033	ACCEPT	Summary: ISCA2 binds iron ions as part of its [2Fe-2S] and [4Fe-4S] cluster-binding capacity. The iron binding is integral to its function in Fe-S cluster assembly. Reason: Iron ion binding is inherent to ISCA2's function as an Fe-S cluster assembly protein. The protein coordinates iron through conserved cysteine residues (Cys79, Cys144, Cys146) as documented in UniProt and structural studies. This is a valid but somewhat generic annotation that is subsumed by the more specific cluster binding annotations. Supporting Evidence: PMID:25347204 ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a dimeric state
GO:0051537 2 iron, 2 sulfur cluster binding	IBA GO_REF:0000033	ACCEPT	Summary: ISCA2 binds [2Fe-2S] clusters as part of its role in Fe-S cluster assembly. The [2Fe-2S] cluster is received from GLRX5 and is an intermediate in [4Fe-4S] assembly (PMID:25347204, PMID:31831856). Reason: [2Fe-2S] cluster binding by ISCA2 is well-documented. ISCA2 can hold a [2Fe-2S] cluster and forms a [2Fe-2S]-bridged heterocomplex with IBA57. The cluster is an intermediate received from GLRX5 that is subsequently converted to [4Fe-4S]. Supporting Evidence: PMID:25347204 ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a dimeric state PMID:31831856 The [2Fe-2S] cluster is out of the ISCA2 core while being shared with IBA57 in the dimer
GO:0051539 4 iron, 4 sulfur cluster binding	IBA GO_REF:0000033	ACCEPT	Summary: ISCA2, as part of the ISCA1:ISCA2 heterodimeric complex, binds [4Fe-4S] clusters that are assembled from two [2Fe-2S] precursors (PMID:25347204). Reason: [4Fe-4S] cluster binding is a core function of the ISCA1:ISCA2 complex. The heterodimeric complex assembles and transiently holds a [4Fe-4S] cluster before transfer to target apo-proteins. Supporting Evidence: PMID:25347204 ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a dimeric state PMID:25347204 the two GRX5-donated [2Fe-2S](2+) clusters generate a [4Fe-4S](2+) cluster
GO:0005739 mitochondrion	IEA GO_REF:0000044	ACCEPT	Summary: IEA annotation for mitochondrial localization based on UniProt subcellular location vocabulary. Consistent with experimental evidence. Reason: This IEA annotation is consistent with the IBA and IDA evidence for mitochondrial localization. While redundant with higher-quality annotations, it provides a valid automatic annotation that does not conflict with established knowledge. Supporting Evidence: PMID:25347204 The generation of [4Fe-4S] clusters in mitochondria critically depends, in both yeast and human cells, on two A-type ISC proteins (in mammals named ISCA1 and ISCA2)
GO:0016226 iron-sulfur cluster assembly	IEA GO_REF:0000002	ACCEPT	Summary: IEA annotation for iron-sulfur cluster assembly based on InterPro domain mapping. Reason: This IEA annotation is correct based on domain analysis (FeS_cluster_insertion domain IPR016092). Consistent with ISCA2's role in Fe-S biogenesis and the IBA annotation for the same term. Supporting Evidence: PMID:25347204 The generation of [4Fe-4S] clusters in mitochondria critically depends, in both yeast and human cells, on two A-type ISC proteins
GO:0046872 metal ion binding	IEA GO_REF:0000043	MARK AS OVER ANNOTATED	Summary: IEA annotation for metal ion binding based on UniProt keyword mapping. Very general annotation subsumed by more specific iron and Fe-S cluster binding terms. Reason: While technically correct (ISCA2 binds iron as part of Fe-S clusters), this term is overly broad and uninformative given the more specific annotations for iron ion binding and Fe-S cluster binding that are already present. It adds little value beyond what is captured by more specific MF terms.
GO:0051536 iron-sulfur cluster binding	IEA GO_REF:0000120	ACCEPT	Summary: IEA annotation for general iron-sulfur cluster binding based on combined IEA methods. Reason: This general Fe-S cluster binding annotation is correct and serves as a parent term encompassing both [2Fe-2S] and [4Fe-4S] cluster binding, which are both relevant to ISCA2 function. More specific child terms are also annotated. Supporting Evidence: PMID:25347204 ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a dimeric state
GO:0120510 mitochondrial [4Fe-4S] assembly complex	IEA GO_REF:0000117	ACCEPT	Summary: IEA annotation indicating ISCA2 is part of the mitochondrial [4Fe-4S] assembly complex, based on ARBA machine learning. Reason: This is an accurate annotation. ISCA2 is indeed a component of the mitochondrial [4Fe-4S] assembly complex (ISCA1:ISCA2 complex) as defined in GO. The GO term definition explicitly states "In humans it consists of ISCA1 and ISCA2." Supporting Evidence: PMID:25347204 We found that (i) ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a dimeric state, and (ii) two molecules of [2Fe-2S](2+) GRX5 donate their cluster to a heterodimeric ISCA1/ISCA2 complex
GO:0005515 protein binding	IPI PMID:25347204 Formation of [4Fe-4S] clusters in the mitochondrial iron-sul...	MODIFY	Summary: IPI annotation for protein binding based on ISCA2 interaction with ISCA1 (Q9BUE6) demonstrated in this study. Reason: The annotation captures a real interaction (ISCA2 with ISCA1), but "protein binding" is uninformative. ISCA2 forms a functional heterodimeric complex with ISCA1 that assembles [4Fe-4S] clusters. This is better captured by the complex membership annotation (GO:0120510) or the identical protein binding annotation for homodimerization. Proposed replacements: mitochondrial [4Fe-4S] assembly complex Supporting Evidence: PMID:25347204 We found that (i) ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a dimeric state, and (ii) two molecules of [2Fe-2S](2+) GRX5 donate their cluster to a heterodimeric ISCA1/ISCA2 complex
GO:0005515 protein binding	IPI PMID:25416956 A proteome-scale map of the human interactome network.	MARK AS OVER ANNOTATED	Summary: IPI annotation for protein binding based on high-throughput interactome mapping (interaction with RNF41/Q9H4P4). Reason: This annotation derives from high-throughput interactome mapping and captures an interaction with RNF41 (E3 ubiquitin ligase). While the interaction may be real, the generic "protein binding" term is uninformative and the biological relevance of ISCA2-RNF41 interaction to ISCA2's core Fe-S assembly function is unclear. Supporting Evidence: PMID:25416956 A proteome-scale map of the human interactome network.
GO:0005515 protein binding	IPI PMID:31831856 Structural properties of [2Fe-2S] ISCA2-IBA57: a complex of ...	MODIFY	Summary: IPI annotation for protein binding based on ISCA2-IBA57 interaction demonstrated by structural and biophysical studies (Nasta et al., 2019). Reason: This captures the important ISCA2-IBA57 interaction, but "protein binding" is uninformative. ISCA2 forms a [2Fe-2S]-bridged heterocomplex with IBA57 that is structurally characterized and functionally important for late-stage Fe-S assembly. Proposed replacements: iron-sulfur cluster chaperone activity Supporting Evidence: PMID:31831856 The [2Fe-2S] cluster is out of the ISCA2 core while being shared with IBA57 in the dimer PMID:31831856 dimeric [2Fe-2S] ISCA2-IBA57 hetero-complex is a physiologically relevant species
GO:0005515 protein binding	IPI PMID:32296183 A reference map of the human binary protein interactome.	MARK AS OVER ANNOTATED	Summary: IPI annotation for multiple protein interactions from high-throughput binary interactome mapping. Reason: This is a high-throughput study identifying multiple interactors. The generic "protein binding" term is uninformative. Many of the reported interactors (e.g., SUOX, GEM, EIF3E) lack clear functional relevance to ISCA2's core Fe-S assembly function and may represent experimental artifacts or transient interactions. Supporting Evidence: PMID:32296183 Apr 8. A reference map of the human binary protein interactome.
GO:0005515 protein binding	IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ...	MARK AS OVER ANNOTATED	Summary: IPI annotation from interactome mapping in the context of neurodegenerative disease protein networks. Reason: This high-throughput interactome study reports multiple ISCA2 interactors, but the generic "protein binding" annotation is uninformative. The biological relevance of these interactions to ISCA2's core Fe-S assembly function is unclear. Supporting Evidence: PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
GO:0005515 protein binding	IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling...	MARK AS OVER ANNOTATED	Summary: IPI annotation from dual proteome-scale network studies showing ISCA2 interactions with IBA57, ISCA1, and RNF41. Reason: While this study confirms biologically relevant interactions (ISCA1, IBA57), the generic "protein binding" term is uninformative. The relevant functional interactions are better captured by complex membership (GO:0120510) and specific binding annotations. Supporting Evidence: PMID:33961781 2021 May 6. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
GO:0005515 protein binding	IPI PMID:39408793 Defects in the Maturation of Mitochondrial Iron-Sulfur Prote...	ACCEPT	Summary: IPI annotation based on ISCA2-IBA57 interaction studies in context of MMDS3 pathogenic variant analysis. Reason: This study specifically characterizes the ISCA2-IBA57 interaction in the context of disease-causing IBA57 variants. While "protein binding" is generic, this annotation has clear functional relevance to understanding ISCA2's role in the late ISC pathway and disease mechanisms. Supporting Evidence: file:human/ISCA2/ISCA2-deep-research-falcon.md ISCA2 forms a dimer and assembles a [2Fe-2S] ISCA2-IBA57 heterocomplex that is oxidation-resistant and can reactivate apo-aconitase PMID:39408793 Defects in the Maturation of Mitochondrial Iron-Sulfur Proteins: Biophysical Investigation of the MMDS3 Causing Gly104Cys Variant of IBA57.
GO:0005515 protein binding	IPI PMID:40205054 Multimodal cell maps as a foundation for structural and func...	MARK AS OVER ANNOTATED	Summary: IPI annotation from multimodal cell mapping study showing ISCA2 interactions. Reason: High-throughput study with generic "protein binding" annotation that is uninformative about ISCA2's specific molecular function. Supporting Evidence: PMID:40205054 Apr 9. Multimodal cell maps as a foundation for structural and functional genomics.
GO:0042802 identical protein binding	IPI PMID:25347204 Formation of [4Fe-4S] clusters in the mitochondrial iron-sul...	ACCEPT	Summary: ISCA2 forms homodimers, as demonstrated in structural and biochemical studies (PMID:25347204, PMID:31831856). Reason: ISCA2 homodimerization is well-documented and functionally relevant. The apo form of ISCA2 is dimeric, and this dimerization is important for its cluster binding and assembly function. Supporting Evidence: PMID:25347204 ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a dimeric state PMID:31831856 ISCA2-IBA57 complex with ISCA2 providing the homodimerization core interface
GO:0042802 identical protein binding	IPI PMID:31831856 Structural properties of [2Fe-2S] ISCA2-IBA57: a complex of ...	ACCEPT	Summary: Structural study (SAXS and modeling) confirming ISCA2 homodimerization as the core interface in the ISCA2-IBA57 complex. Reason: This study provides structural evidence for ISCA2 homodimerization. The ISCA2 dimer provides the core interface for complex formation with IBA57. Supporting Evidence: PMID:31831856 ISCA2-IBA57 complex with ISCA2 providing the homodimerization core interface
GO:0005739 mitochondrion	IDA PMID:22323289 The human mitochondrial ISCA1, ISCA2, and IBA57 proteins are...	ACCEPT	Summary: Direct experimental evidence (IDA) for mitochondrial localization from the foundational study establishing ISCA2's role in [4Fe-4S] protein maturation. Reason: This is high-quality experimental evidence for mitochondrial localization from the key study by Sheftel et al. that established the function of human ISCA1, ISCA2, and IBA57 in [4Fe-4S] protein maturation. Supporting Evidence: file:human/ISCA2/ISCA2-deep-research-falcon.md ISCA2 functions in the mitochondrial matrix, evidenced by its role in mitochondrial [4Fe-4S] client maturation PMID:22323289 Feb 9. The human mitochondrial ISCA1, ISCA2, and IBA57 proteins are required for [4Fe-4S] protein maturation.
GO:0051604 protein maturation	IDA PMID:25347204 Formation of [4Fe-4S] clusters in the mitochondrial iron-sul...	ACCEPT	Summary: Direct experimental evidence that ISCA2 is involved in [4Fe-4S] protein maturation by assembling clusters for transfer to target apo-proteins. Reason: This annotation is based on biochemical reconstitution studies showing the ISCA1:ISCA2 complex assembles [4Fe-4S] clusters for transfer to target proteins. Supporting Evidence: PMID:25347204 These findings imply that such heterodimeric complex is the functional unit in mitochondria receiving [2Fe-2S] clusters from hGRX5 and assembling [4Fe-4S] clusters before their transfer to the final target apo proteins
GO:0051604 protein maturation	NAS PMID:31831856 Structural properties of [2Fe-2S] ISCA2-IBA57: a complex of ...	ACCEPT	Summary: Non-traceable author statement annotation for protein maturation function based on the ISCA2-IBA57 structural study. Reason: While NAS is a weaker evidence code, the annotation is consistent with the well-established role of ISCA2 in [4Fe-4S] protein maturation. The referenced paper provides structural context for understanding how ISCA2 contributes to this process. Supporting Evidence: PMID:31831856 dimeric [2Fe-2S] ISCA2-IBA57 hetero-complex is a physiologically relevant species
GO:0005739 mitochondrion	HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an...	ACCEPT	Summary: High-throughput proteomics study confirming ISCA2 as part of the high-confidence mitochondrial proteome. Reason: This high-quality proteomics study provides additional support for mitochondrial localization, consistent with other experimental evidence. Supporting Evidence: PMID:34800366 Epub 2021 Nov 19. Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context.
GO:0120510 mitochondrial [4Fe-4S] assembly complex	IDA PMID:25347204 Formation of [4Fe-4S] clusters in the mitochondrial iron-sul...	ACCEPT	Summary: Direct experimental evidence that ISCA2 is part of the mitochondrial [4Fe-4S] assembly complex (ISCA1:ISCA2 heterodimer) that assembles [4Fe-4S] clusters. Reason: This is a key annotation capturing ISCA2's core function. The study demonstrates that the ISCA1:ISCA2 heterodimeric complex is the functional unit for [4Fe-4S] cluster assembly. Supporting Evidence: PMID:25347204 We found that (i) ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a dimeric state, and (ii) two molecules of [2Fe-2S](2+) GRX5 donate their cluster to a heterodimeric ISCA1/ISCA2 complex
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-8878815	ACCEPT	Summary: Reactome pathway annotation indicating ISCA2 functions in the mitochondrial matrix, where [4Fe-4S] cluster formation occurs on the ISCA1:ISCA2 complex. Reason: The mitochondrial matrix localization is consistent with ISCA2's role in late-stage Fe-S cluster assembly, which occurs in the matrix compartment. Reactome provides curated pathway context. Supporting Evidence: Reactome:R-HSA-8878815 Formation of 4Fe-4S cluster on ISCA1:ISCA2
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-9854984	ACCEPT	Summary: Reactome annotation for mitochondrial matrix localization in context of Fe-S cluster transfer to SDHB. Reason: Consistent with ISCA2's role in maturation of mitochondrial [4Fe-4S] proteins including succinate dehydrogenase complex subunits. Supporting Evidence: Reactome:R-HSA-9854984 Transfer of Fe-S clusters to SDHB
GO:0044572 [4Fe-4S] cluster assembly	IDA PMID:25347204 Formation of [4Fe-4S] clusters in the mitochondrial iron-sul...	NEW	Summary: NEW ANNOTATION: ISCA2 is involved in [4Fe-4S] cluster assembly as a biological process. The ISCA1:ISCA2 complex assembles [4Fe-4S] clusters from [2Fe-2S] precursors. Reason: The existing annotations include the general term GO:0016226 (iron-sulfur cluster assembly), but ISCA2's specific function is [4Fe-4S] cluster assembly, which is captured by the more precise child term GO:0044572. Supporting Evidence: PMID:25347204 This complex acts as an "assembler" of [4Fe-4S] clusters; i.e., the two GRX5-donated [2Fe-2S](2+) clusters generate a [4Fe-4S](2+) cluster

Core Functions

ISCA2 is a core component of the late-stage mitochondrial ISC pathway, functioning specifically in [4Fe-4S] cluster assembly. Biochemical reconstitution studies (PMID:25347204) demonstrated that the ISCA1:ISCA2 heterodimeric complex receives [2Fe-2S] clusters from GLRX5 and assembles them into [4Fe-4S] clusters through reductive fusion, with electrons supplied by FDX2/FDXR.

Molecular Function:

4 iron, 4 sulfur cluster binding

Directly Involved In:

[4Fe-4S] cluster assembly protein maturation

Cellular Locations:

mitochondrial matrix

In Complex:

mitochondrial [4Fe-4S] assembly complex

Supporting Evidence:

PMID:25347204
This complex acts as an "assembler" of [4Fe-4S] clusters; i.e., the two GRX5-donated [2Fe-2S](2+) clusters generate a [4Fe-4S](2+) cluster
file:human/ISCA2/ISCA2-deep-research-falcon.md
ISCA2 is a mitochondrial A-type Fe-S assembly factor in the HesB/IscA family. It acts as a late-acting secondary carrier in the ISC pathway

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000043

Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping

GO_REF:0000117

Electronic Gene Ontology annotations created by ARBA machine learning models

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:22323289

The human mitochondrial ISCA1, ISCA2, and IBA57 proteins are required for [4Fe-4S] protein maturation.

Established that ISCA1, ISCA2, and IBA57 are required for mitochondrial [4Fe-4S] protein maturation

"The human mitochondrial ISCA1, ISCA2, and IBA57 proteins are required for [4Fe-4S] protein maturation"
RNAi depletion causes loss of [4Fe-4S] enzyme activities (aconitase, lipoic acid synthase)

"The activities of mitochondrial [4Fe-4S] proteins, including aconitase, respiratory complex I, and lipoic acid synthase, were diminished following depletion of the three proteins"
Confirmed mitochondrial localization of ISCA2

"We conclude that all three ISC proteins are located in mitochondria"

PMID:25347204

Formation of [4Fe-4S] clusters in the mitochondrial iron-sulfur cluster assembly machinery.

ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a dimeric state

"ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a dimeric state"
ISCA1:ISCA2 heterodimeric complex receives [2Fe-2S] clusters from GRX5

"two molecules of [2Fe-2S](2+) GRX5 donate their cluster to a heterodimeric ISCA1/ISCA2 complex"
The complex assembles [4Fe-4S] clusters from two [2Fe-2S] precursors

"the two GRX5-donated [2Fe-2S](2+) clusters generate a [4Fe-4S](2+) cluster"
Established the ISCA1:ISCA2 complex as the functional unit for [4Fe-4S] assembly

"These findings imply that such heterodimeric complex is the functional unit in mitochondria"

PMID:25416956

A proteome-scale map of the human interactome network.

High-throughput interactome mapping identified ISCA2 protein interactions

PMID:31831856

Structural properties of [2Fe-2S] ISCA2-IBA57: a complex of the mitochondrial iron-sulfur cluster assembly machinery.

ISCA2 forms homodimer that provides core interface for IBA57 interaction

"ISCA2-IBA57 complex with ISCA2 providing the homodimerization core interface"
Characterized [2Fe-2S]-bridged ISCA2-IBA57 heterocomplex structure by SAXS

"The [2Fe-2S] cluster is out of the ISCA2 core while being shared with IBA57 in the dimer"
Complex forms dimer of dimers (heterotetramer)

"dimeric [2Fe-2S] ISCA2-IBA57 hetero-complex is a physiologically relevant species"
Defined molecular basis for pathogenic IBA57 Arg146Trp mutation

"The specific interaction pattern identified from the dimeric [2Fe-2S]2+ ISCA2-IBA57 structural model allowed us to define the molecular grounds of the pathogenic Arg146Trp mutation of IBA57"

PMID:32296183

A reference map of the human binary protein interactome.

High-throughput binary interactome mapping

PMID:32814053

Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins.

ISCA2 interactors identified in neurodegenerative disease protein network context

PMID:33961781

Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.

Confirmed ISCA2 interactions with ISCA1 and IBA57

PMID:34800366

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

ISCA2 identified as high-confidence mitochondrial protein

PMID:39408793

Defects in the Maturation of Mitochondrial Iron-Sulfur Proteins: Biophysical Investigation of the MMDS3 Causing Gly104Cys Variant of IBA57.

Characterization of ISCA2-IBA57 interaction in context of disease variants

PMID:40205054

Multimodal cell maps as a foundation for structural and functional genomics.

ISCA2 protein interactions from multimodal cell mapping

Reactome:R-HSA-8878815

Formation of 4Fe-4S cluster on ISCA1:ISCA2

Pathway curation placing ISCA2 in [4Fe-4S] cluster formation reaction

Reactome:R-HSA-9854984

Transfer of Fe-S clusters to SDHB

ISCA2 involved in pathway for Fe-S cluster transfer to respiratory chain components

📚 Additional Documentation

Deep Research Falcon

(ISCA2-deep-research-falcon.md)

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template_file: templates/gene_research_go_focused.md
template_variables:
organism: human
gene_id: ISCA2
gene_symbol: ISCA2
uniprot_accession: Q86U28
protein_description: 'RecName: Full=Iron-sulfur cluster assembly 2 homolog, mitochondrial;
AltName: Full=HESB-like domain-containing protein 1; Flags: Precursor;'
gene_info: Name=ISCA2; Synonyms=HBLD1;
organism_full: Homo sapiens (Human).
protein_family: Belongs to the HesB/IscA family. .
protein_domains: FeS_biogenesis. (IPR000361); FeS_cluster_insertion. (IPR016092);
FeS_cluster_insertion_CS. (IPR017870); HesB-like_dom_sf. (IPR035903); Fe-S_biosyn
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Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

UniProt Accession: Q86U28
Protein Description: RecName: Full=Iron-sulfur cluster assembly 2 homolog, mitochondrial; AltName: Full=HESB-like domain-containing protein 1; Flags: Precursor;
Gene Information: Name=ISCA2; Synonyms=HBLD1;
Organism (full): Homo sapiens (Human).
Protein Family: Belongs to the HesB/IscA family. .
Key Domains: FeS_biogenesis. (IPR000361); FeS_cluster_insertion. (IPR016092); FeS_cluster_insertion_CS. (IPR017870); HesB-like_dom_sf. (IPR035903); Fe-S_biosyn (PF01521)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "ISCA2" matches the protein description above
Verify the organism is correct: Homo sapiens (Human).
Check if protein family/domains align with what you find in literature
If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'ISCA2' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene ISCA2 (gene ID: ISCA2, UniProt: Q86U28) in human.

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.

Output

Question: You are an expert researcher providing comprehensive, well-cited information.

Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies

Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

UniProt Accession: Q86U28
Protein Description: RecName: Full=Iron-sulfur cluster assembly 2 homolog, mitochondrial; AltName: Full=HESB-like domain-containing protein 1; Flags: Precursor;
Gene Information: Name=ISCA2; Synonyms=HBLD1;
Organism (full): Homo sapiens (Human).
Protein Family: Belongs to the HesB/IscA family. .
Key Domains: FeS_biogenesis. (IPR000361); FeS_cluster_insertion. (IPR016092); FeS_cluster_insertion_CS. (IPR017870); HesB-like_dom_sf. (IPR035903); Fe-S_biosyn (PF01521)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "ISCA2" matches the protein description above
Verify the organism is correct: Homo sapiens (Human).
Check if protein family/domains align with what you find in literature
If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

Research Target:

Please provide a comprehensive research report on the gene ISCA2 (gene ID: ISCA2, UniProt: Q86U28) in human.

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.

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.

Plan and verification
- Identity verification: ISCA2 matches UniProt Q86U28. Literature consistently identifies human ISCA2 as a mitochondrial A-type iron–sulfur (Fe–S) assembly protein of the HesB/IscA family that functions in late steps of [4Fe-4S] cluster biogenesis, partnering with ISCA1 and IBA57 (IUBMB Life 2022, doi:10.1002/iub.2597; Trends Biochem Sci 2020, doi:10.1016/j.tibs.2020.02.001). The organism is Homo sapiens, mitochondrial localization is established by functional studies and disease phenotypes linked to mitochondrial [4Fe-4S] maturation defects (Human Mutation 2018, doi:10.1002/humu.23396). These align with the FeS_biogenesis/HesB-like domain context provided. (maio2020outliningthecomplex pages 10-12, alaimo2018loss‐of‐functionmutationsin pages 1-5)

Comprehensive research report on human ISCA2 (Q86U28)

1) Key concepts and definitions
- ISCA2 is a mitochondrial A-type Fe–S assembly factor in the HesB/IscA family. It acts as a late-acting “secondary carrier” in the ISC pathway, coordinating with ISCA1 and IBA57 to assemble [4Fe-4S] clusters from [2Fe-2S] precursors initially built on ISCU and transferred via GLRX5. Review articles position ISCA2 within this late maturation module and link ISCA2 variants to Multiple Mitochondrial Dysfunction Syndrome type 4 (MMDS4; OMIM #616370). URLs: IUBMB Life (Jan 2022) https://doi.org/10.1002/iub.2597; Trends in Biochemical Sciences (May 2020) https://doi.org/10.1016/j.tibs.2020.02.001. (maio2022mammalianironsulfur pages 1-2, maio2020outliningthecomplex pages 10-12)
- Cellular localization: ISCA2 functions in the mitochondrial matrix, evidenced by its role in mitochondrial [4Fe-4S] client maturation and the mitochondrial bioenergetic defects observed upon loss-of-function. URL: Human Mutation (Jan 2018) https://doi.org/10.1002/humu.23396. (alaimo2018loss‐of‐functionmutationsin pages 1-5, alaimo2018loss‐of‐functionmutationsin pages 17-21)
- Functional definition: ISCA2 participates in reductive coupling of two [2Fe-2S] units into [4Fe-4S] clusters in conjunction with ISCA1 and IBA57, using electrons from ferredoxin FDX2 via FDXR, with GLRX5 as the physiological [2Fe-2S] donor. URL: PNAS (Aug 2020) https://doi.org/10.1073/pnas.2003982117. (weiler2020mitochondrial[4fe4s]protein pages 1-1)

2) Mechanism and current understanding (with recent developments)
- Late ISC reconstitution: A fully reconstituted system showed that GLRX5 delivers [2Fe-2S] to the ISCA1–ISCA2–IBA57 module, which requires electron input from mitochondrial FDX2 (not FDX1) via FDXR to drive reductive fusion to [4Fe-4S]. This reconstitution activated mitochondrial [4Fe-4S] aconitase without artificial reductants, establishing physiological specificity and the necessity of IBA57 in the reaction. URL: PNAS 2020 https://doi.org/10.1073/pnas.2003982117. (weiler2020mitochondrial[4fe4s]protein pages 1-1)
- Structural/organizational insights: SAXS and integrative modeling indicate ISCA2 is dimeric (apo) and forms a [2Fe-2S]-bridged heterocomplex with monomeric IBA57 that is oxidation-resistant and capable of reactivating apo-aconitase. The ISCA2–IBA57 complex shares a [2Fe-2S] cluster but, with only four cysteines, is not itself a [4Fe-4S] assembly site; conversely, an ISCA2 homodimer with “facing cysteines” could support [4Fe-4S] cluster assembly, suggesting alternative routes and repair roles. URL: Scientific Reports (Dec 2019) https://doi.org/10.1038/s41598-019-55313-5. (nasta2019structuralpropertiesof pages 7-8, nasta2019structuralpropertiesof pages 10-11)
- GLRX5 vs direct [2Fe-2S] delivery: The same reconstitution work showed rapid, spontaneous transfer of [2Fe-2S] from GLRX5 to [2Fe-2S] apoproteins without additional ISC factors, highlighting that ISCA2’s primary role is not direct [2Fe-2S] delivery but participation in [4Fe-4S] cluster formation. URL: PNAS 2020 https://doi.org/10.1073/pnas.2003982117. (weiler2020mitochondrial[4fe4s]protein pages 1-1)
- Context-dependent essentiality debate: Reviews highlight mixed in vivo data—some knockdowns in mouse skeletal muscle and neurons suggest ISCA1 is essential for [4Fe-4S] biogenesis, whereas ISCA2/IBA57 are less critical in those specific contexts, implying tissue- or pathway-specific roles. These analyses reinforce that ISCA1/ISCA2/IBA57 form a dynamic late ISC network whose precise client spectrum is still being resolved. URLs: Trends Biochem Sci (May 2020) https://doi.org/10.1016/j.tibs.2020.02.001; IUBMB Life (Jan 2022) https://doi.org/10.1002/iub.2597. (maio2020outliningthecomplex pages 10-12, maio2022mammalianironsulfur pages 1-2)
- 2023–2024 updates: A 2024 review aggregates MMDS insights and reaffirms the ISCA2–IBA57 heterocomplex and MMDS4 phenotype; it also notes decreased lipoylation as a consistent biochemical sign of failed [4Fe-4S] incorporation in LIAS-dependent pathways. URL: 2024 review (Bargagna 2024; review DOI not provided in excerpt). (bargagna2024molecularpathwaysforb pages 16-20, bargagna2024molecularpathwaysfor pages 16-20)

3) Pathways and substrates/clients
- Upstream: [2Fe-2S] synthesis on ISCU and relay to GLRX5.
- Late-acting module: ISCA1–ISCA2–IBA57 uses GLRX5-donated [2Fe-2S] and FDX2/FDXR electrons for reductive fusion to [4Fe-4S]; this step is differentiated from [2Fe-2S] delivery, which does not require the ISCA module. URL: PNAS 2020 https://doi.org/10.1073/pnas.2003982117. (weiler2020mitochondrial[4fe4s]protein pages 1-1)
- Clients: [4Fe-4S]-dependent mitochondrial enzymes such as aconitase and lipoic acid synthase (LIAS) are impacted when ISCA2 is deficient, leading to reduced protein lipoylation and downstream defects in PDH, KGDH, and the glycine cleavage system. URLs: Human Mutation (Jan 2018) https://doi.org/10.1002/humu.23396; Biomedicines (Aug 2021) https://doi.org/10.3390/biomedicines9080989. (alaimo2018loss‐of‐functionmutationsin pages 17-21, maio2022mammalianironsulfur pages 1-2)

4) Disease associations, clinical phenotypes, and biomarkers
- MMDS4 due to ISCA2: Bi-allelic ISCA2 missense variants, notably c.229G>A (p.Gly77Ser), cause an infantile-onset leukodystrophy characterized by developmental regression, hypotonia, spasticity, optic atrophy, and white-matter disease, with biomarkers including hyperglycinemia, elevated lactate/pyruvate, and low CSF 5-methyltetrahydrofolate; loss of protein lipoylation is characteristic. URL: Human Mutation (Jan 2018) https://doi.org/10.1002/humu.23396; Biomedicines (Aug 2021) https://doi.org/10.3390/biomedicines9080989. (alaimo2018loss‐of‐functionmutationsin pages 1-5, alaimo2018loss‐of‐functionmutationsin pages 17-21, maio2022mammalianironsulfur pages 1-2)
- Mitochondrial and bioenergetic deficits: Patient fibroblasts and ISCA2 knockdown models show decreased mitochondrial membrane potential, impaired basal and maximal respiration, reduced ATP production (~50% of control), diminished spare respiratory capacity (~25% of control), and decreased activities/proteins of ETC complexes—particularly complex II and IV (to ~60–70% of control)—with mitochondrial network fragmentation and mtDNA depletion (~25% of control). URL: Human Mutation (Jan 2018) https://doi.org/10.1002/humu.23396. (alaimo2018loss‐of‐functionmutationsin pages 13-17, alaimo2018loss‐of‐functionmutationsin pages 17-21)
- Case counts and 2024 update: A 2024 review reports approximately 24 MMDS4 patients described to date, with consistent early-onset neurological phenotypes and decreased levels of lipoylated proteins. 2015 reports identified homozygous p.Gly77Ser in seven patients; the accumulated total is summarized in 2024. URL: 2024 review (Bargagna 2024; DOI not provided in excerpt). (bargagna2024molecularpathwaysforb pages 16-20, bargagna2024molecularpathwaysfor pages 16-20)

5) Expert opinions and analysis from authoritative sources
- Mechanistic consensus: The ISCA1–ISCA2–IBA57 node is required for assembling [4Fe-4S] clusters in mitochondria; GLRX5 is the [2Fe-2S] donor; electrons are supplied by the FDX2–FDXR system; [2Fe-2S] transfer to [2Fe-2S] targets proceeds without this late module. This delineates a mechanistic division of labor in Fe–S biogenesis. URL: PNAS (Aug 2020) https://doi.org/10.1073/pnas.2003982117. (weiler2020mitochondrial[4fe4s]protein pages 1-1)
- Tissue/context specificity: Reviews emphasize a dynamic, context-dependent network, with some models indicating ISCA1 prioritization in certain tissues, and ISCA2/IBA57 forming an oxidation-resistant complex likely supporting specific clients or stress conditions. URLs: Trends Biochem Sci 2020 https://doi.org/10.1016/j.tibs.2020.02.001; IUBMB Life 2022 https://doi.org/10.1002/iub.2597; Scientific Reports 2019 https://doi.org/10.1038/s41598-019-55313-5. (maio2020outliningthecomplex pages 10-12, maio2022mammalianironsulfur pages 1-2, nasta2019structuralpropertiesof pages 7-8)

6) Current applications and real-world implementations
- Diagnostics: Recognition of the MMDS biochemical signature—elevated CSF glycine and lactate/pyruvate, defective protein lipoylation, and characteristic MRI features—guides genetic testing (targeted panels/WES) for ISCA2 variants. Systematic reviews consolidate these markers and support standardized diagnostic workflows. URL: Biomedicines (Aug 2021) https://doi.org/10.3390/biomedicines9080989. (maio2022mammalianironsulfur pages 1-2)
- Functional validation: Cell-based assays of lipoylation status, respiratory complex activities, and mtDNA copy number in patient-derived fibroblasts or knockdown lines are used to validate pathogenicity and define the mechanistic consequences of ISCA2 variants. URL: Human Mutation (Jan 2018) https://doi.org/10.1002/humu.23396. (alaimo2018loss‐of‐functionmutationsin pages 17-21)
- Research tools: The reconstituted late ISC system and oxidation-resistant ISCA2–IBA57 complexes enable mechanistic dissection of client maturation and stress responses. URLs: PNAS (Aug 2020) https://doi.org/10.1073/pnas.2003982117; Scientific Reports (Dec 2019) https://doi.org/10.1038/s41598-019-55313-5. (weiler2020mitochondrial[4fe4s]protein pages 1-1, nasta2019structuralpropertiesof pages 7-8)

7) Relevant statistics and data from recent studies
- MMDS4 prevalence in literature: ~24 patients summarized by 2024, most with homozygous or compound-heterozygous ISCA2 variants, notably Gly77Ser as a recurrent founder allele; early onset (first year) with psychomotor impairment, spasticity, optic atrophy; decreased lipoylation common. 2015 initial series: seven patients with Gly77Ser. URL: 2024 review (Bargagna 2024; DOI not provided in excerpt). (bargagna2024molecularpathwaysforb pages 16-20, bargagna2024molecularpathwaysfor pages 16-20)
- Quantitative cellular phenotypes in ISCA2 deficiency: In patient fibroblasts, ATP production ~50% of control, spare respiratory capacity ~25% of control; ETC complex II and IV activities reduced to ~60–70% of control; mtDNA copy number ~25% of control; robust loss of protein lipoylation. URL: Human Mutation (Jan 2018) https://doi.org/10.1002/humu.23396. (alaimo2018loss‐of‐functionmutationsin pages 13-17, alaimo2018loss‐of‐functionmutationsin pages 17-21)

8) Open questions and debates
- Essentiality and client specificity: The ISCA1 vs ISCA2 essentiality discrepancy in specific tissues suggests specialization and/or redundancy under certain physiological conditions; defining exact client sets for the ISCA2–IBA57 vs ISCA1–ISCA2 routes remains a priority. URLs: Trends Biochem Sci (May 2020) https://doi.org/10.1016/j.tibs.2020.02.001; IUBMB Life (Jan 2022) https://doi.org/10.1002/iub.2597. (maio2020outliningthecomplex pages 10-12, maio2022mammalianironsulfur pages 1-2)
- Structural resolution: The ISCA2–IBA57 complex is characterized by SAXS and modeling; higher-resolution structures in human mitochondria and direct visualization of [4Fe-4S] assembly on ISCA dimers in situ would refine mechanistic models. URL: Scientific Reports (Dec 2019) https://doi.org/10.1038/s41598-019-55313-5. (nasta2019structuralpropertiesof pages 7-8)

Embedded artifact summarizing key studies
| Year | Citation (first author et al.) | Focus | Major Finding(s) on ISCA2/late ISC | Disease/Clinical Notes | URL/DOI | Publication date (month/year) |
|---|---|---|---|---|---|---|
| 2019 | Nasta et al. | Structural/biophysical study of ISCA2–IBA57 | ISCA2 forms a dimer and assembles a [2Fe-2S] ISCA2–IBA57 heterocomplex that is oxidation-resistant and can reactivate apo-aconitase, supporting a role in late-stage [4Fe-4S] biogenesis (structural models from SAXS/HADDOCK). (nasta2019structuralpropertiesof pages 7-8, nasta2019structuralpropertiesof pages 10-11) | Pathogenic IBA57 variants disrupt the complex, linking structure to MMDS phenotypes. | https://doi.org/10.1038/s41598-019-55313-5 | Dec/2019 |
| 2020 | Weiler et al. | Biochemical reconstitution of [4Fe-4S] assembly | GLRX5 is the physiological [2Fe-2S] donor and ISCA1–ISCA2–IBA57 mediate reductive fusion of two [2Fe-2S] clusters into [4Fe-4S] using electrons from mitochondrial FDX2/FDXR; FDX1 cannot substitute. (weiler2020mitochondrial[4fe4s]protein pages 1-1) | Mechanistic basis for late ISC defects implicated in MMDS. | https://doi.org/10.1073/pnas.2003982117 | Aug/2020 |
| 2020 | Maio & Rouault | Review: mammalian ISC pathways | Summarizes late ISC as ISCA1/ISCA2/IBA57-mediated [4Fe-4S] assembly with ISCA2 forming an IBA57-stabilized heterocomplex; notes tissue/context-dependent debate on ISCA1 vs ISCA2 essentiality. (maio2020outliningthecomplex pages 10-12) | Places ISCA2 in the MMDS disease framework; highlights uncertain essentiality across tissues. | https://doi.org/10.1016/j.tibs.2020.02.001 | May/2020 |
| 2018 | Alaimo et al. | Clinical & cellular characterization of ISCA2 deficiency | Biallelic ISCA2 (p.Gly77Ser) causes selective impairment of 4Fe-4S-dependent activities, loss of protein lipoylation, impaired respiration and mtDNA depletion, linking ISCA2 loss to defective [4Fe-4S] biogenesis. (alaimo2018loss‐of‐functionmutationsin pages 1-5, alaimo2018loss‐of‐functionmutationsin pages 13-17, alaimo2018loss‐of‐functionmutationsin pages 17-21) | Describes MMDS4: infantile leukodystrophy with hyperglycinemia, optic atrophy, spasticity, lactate peak; mtDNA depletion observed. | https://doi.org/10.1002/humu.23396 | Jan/2018 |
| 2021 | Lebigot et al. | Systematic review of MMDS1–5 | Reviews ISCA2 among late-acting 4Fe-4S maturation factors and summarizes common biomarkers (high lactate/pyruvate/glycine, defective lipoylation) and neuroimaging features of MMDS. (maio2022mammalianironsulfur pages 1-2) | Clinical synthesis useful for diagnosis and genetic testing of MMDS including ISCA2-related cases. | https://doi.org/10.3390/biomedicines9080989 | Aug/2021 |
| 2022 | Maio & Rouault | Update: mammalian Fe-S biogenesis & disease | Reiterates ISCA2 as a secondary carrier in [4Fe-4S] assembly, emphasizes GLRX5→ISCA1/2 pathway and clinical links between ISCA2 mutations and MMDS4. (maio2020outliningthecomplex pages 10-12, maio2022mammalianironsulfur pages 1-2) | Frames ISCA2 within MMDS etiologies and highlights gaps in assigning specific downstream targets. | https://doi.org/10.1002/iub.2597 | Jan/2022 |
| 2022 | Selvanathan & Sankaran | Review: ISC biogenesis & neurological disorders | Describes late ISC conversion of [2Fe-2S]→[4Fe-4S] by ISCA1/ISCA2/IBA57 with GLRX5 as donor and FDX2/FDXR supplying electrons; lists MMDS4 neurological phenotypes and biomarkers. (selvanathan2022mitochondrialironsulfurcluster pages 3-4) | Summarizes neurologic manifestations (developmental regression, optic atrophy, spasticity) and biochemical markers (CSF glycine, lactate). | https://doi.org/10.1016/j.mito.2021.10.004 | Jan/2022 |
| 2021 | Zhang et al. | Review/analysis of mitochondrial ISC transfer | Discusses models for ISCA2–IBA57 organization and alternative late-stage [4Fe-4S] assembly routes (ISCA1–ISCA2 vs ISCA2–IBA57) and functional implications. (nasta2019structuralpropertiesof pages 10-11) | Provides modeling/context that informs how ISCA2 perturbation may produce distinct MMDS features. | https://doi.org/10.52601/bpr.2021.200038 | Apr/2021 |
| 2024 | Bargagna (review) | 2024 review of Fe‑S maturation pathways | Reports cumulative case count for MMDS4 (~24 patients) and reiterates that ISCA2 variants (notably Gly77Ser) correlate with early-onset spasticity/optic atrophy and decreased lipoylated proteins. (bargagna2024molecularpathwaysforb pages 16-20, bargagna2024molecularpathwaysfor pages 16-20) | Recent case-count update and clinical pattern summary for ISCA2-associated MMDS4. | review (2024) — DOI/URL not provided in source excerpt | 2024 |

Table: Concise table summarizing primary studies and reviews on human ISCA2 (Q86U28), highlighting structural, mechanistic, and clinical findings relevant to late mitochondrial Fe–S ([4Fe-4S]) biogenesis and MMDS4; citations link to gathered evidence (context IDs).

Conclusions
Human ISCA2 (Q86U28) is a mitochondrial A-type ISC protein of the HesB/IscA family that cooperates with ISCA1 and IBA57 to assemble [4Fe-4S] clusters from GLRX5-derived [2Fe-2S] units, driven by electrons from FDX2/FDXR. It does not appear to be required for direct [2Fe-2S] delivery to [2Fe-2S] clients. Structural work supports an oxidation-resistant [2Fe-2S]-bridged ISCA2–IBA57 complex and suggests alternative assembly/repair routes via ISCA2 homodimers. Pathogenic ISCA2 variants cause MMDS4 with early-onset leukodystrophy, loss of protein lipoylation, bioenergetic failure, and mtDNA depletion. Recent reviews (2024) tally ~24 reported cases and consolidate a consistent biomarker/phenotypic spectrum. Continued efforts focus on resolving client specificity and tissue-context requirements for ISCA2 function. URLs: PNAS 2020 https://doi.org/10.1073/pnas.2003982117; Scientific Reports 2019 https://doi.org/10.1038/s41598-019-55313-5; Trends Biochem Sci 2020 https://doi.org/10.1016/j.tibs.2020.02.001; IUBMB Life 2022 https://doi.org/10.1002/iub.2597; Biomedicines 2021 https://doi.org/10.3390/biomedicines9080989; Human Mutation 2018 https://doi.org/10.1002/humu.23396; 2024 review (Bargagna 2024). (weiler2020mitochondrial[4fe4s]protein pages 1-1, nasta2019structuralpropertiesof pages 7-8, maio2020outliningthecomplex pages 10-12, maio2022mammalianironsulfur pages 1-2, alaimo2018loss‐of‐functionmutationsin pages 17-21, bargagna2024molecularpathwaysforb pages 16-20)

References

(maio2020outliningthecomplex pages 10-12): Nunziata Maio and Tracey A. Rouault. Outlining the complex pathway of mammalian fe-s cluster biogenesis. Trends in biochemical sciences, 45 5:411-426, May 2020. URL: https://doi.org/10.1016/j.tibs.2020.02.001, doi:10.1016/j.tibs.2020.02.001. This article has 137 citations and is from a domain leading peer-reviewed journal.
(alaimo2018loss‐of‐functionmutationsin pages 1-5): Joseph T. Alaimo, Arnaud Besse, Charlotte L. Alston, Ki Pang, Vivek Appadurai, Monisha Samanta, Patroula Smpokou, Robert McFarland, Robert W. Taylor, and Penelope E. Bonnen. Loss‐of‐function mutations in isca2 disrupt 4fe–4s cluster machinery and cause a fatal leukodystrophy with hyperglycinemia and mtdna depletion. Human Mutation, 39:537-549, Jan 2018. URL: https://doi.org/10.1002/humu.23396, doi:10.1002/humu.23396. This article has 30 citations and is from a domain leading peer-reviewed journal.
(maio2022mammalianironsulfur pages 1-2): Nunziata Maio and Tracey A. Rouault. Mammalian iron sulfur cluster biogenesis and human diseases. IUBMB Life, 74:705-714, Jan 2022. URL: https://doi.org/10.1002/iub.2597, doi:10.1002/iub.2597. This article has 26 citations and is from a peer-reviewed journal.
(alaimo2018loss‐of‐functionmutationsin pages 17-21): Joseph T. Alaimo, Arnaud Besse, Charlotte L. Alston, Ki Pang, Vivek Appadurai, Monisha Samanta, Patroula Smpokou, Robert McFarland, Robert W. Taylor, and Penelope E. Bonnen. Loss‐of‐function mutations in isca2 disrupt 4fe–4s cluster machinery and cause a fatal leukodystrophy with hyperglycinemia and mtdna depletion. Human Mutation, 39:537-549, Jan 2018. URL: https://doi.org/10.1002/humu.23396, doi:10.1002/humu.23396. This article has 30 citations and is from a domain leading peer-reviewed journal.
(weiler2020mitochondrial[4fe4s]protein pages 1-1): Benjamin Dennis Weiler, Marie-Christin Brück, Isabell Kothe, Eckhard Bill, Roland Lill, and Ulrich Mühlenhoff. Mitochondrial [4fe-4s] protein assembly involves reductive [2fe-2s] cluster fusion on isca1–isca2 by electron flow from ferredoxin fdx2. Proceedings of the National Academy of Sciences, 117:20555-20565, Aug 2020. URL: https://doi.org/10.1073/pnas.2003982117, doi:10.1073/pnas.2003982117. This article has 113 citations and is from a highest quality peer-reviewed journal.
(nasta2019structuralpropertiesof pages 7-8): Veronica Nasta, Stefano Da Vela, Spyridon Gourdoupis, Simone Ciofi-Baffoni, Dmitri I. Svergun, and Lucia Banci. Structural properties of [2fe-2s] isca2-iba57: a complex of the mitochondrial iron-sulfur cluster assembly machinery. Scientific Reports, Dec 2019. URL: https://doi.org/10.1038/s41598-019-55313-5, doi:10.1038/s41598-019-55313-5. This article has 27 citations and is from a peer-reviewed journal.
(nasta2019structuralpropertiesof pages 10-11): Veronica Nasta, Stefano Da Vela, Spyridon Gourdoupis, Simone Ciofi-Baffoni, Dmitri I. Svergun, and Lucia Banci. Structural properties of [2fe-2s] isca2-iba57: a complex of the mitochondrial iron-sulfur cluster assembly machinery. Scientific Reports, Dec 2019. URL: https://doi.org/10.1038/s41598-019-55313-5, doi:10.1038/s41598-019-55313-5. This article has 27 citations and is from a peer-reviewed journal.
(bargagna2024molecularpathwaysforb pages 16-20): B Bargagna. Molecular pathways for the maturation of mitochondrial and cytosolic human fe-s proteins. Unknown journal, 2024.
(bargagna2024molecularpathwaysfor pages 16-20): B Bargagna. Molecular pathways for the maturation of mitochondrial and cytosolic human fe-s proteins. Unknown journal, 2024.
(alaimo2018loss‐of‐functionmutationsin pages 13-17): Joseph T. Alaimo, Arnaud Besse, Charlotte L. Alston, Ki Pang, Vivek Appadurai, Monisha Samanta, Patroula Smpokou, Robert McFarland, Robert W. Taylor, and Penelope E. Bonnen. Loss‐of‐function mutations in isca2 disrupt 4fe–4s cluster machinery and cause a fatal leukodystrophy with hyperglycinemia and mtdna depletion. Human Mutation, 39:537-549, Jan 2018. URL: https://doi.org/10.1002/humu.23396, doi:10.1002/humu.23396. This article has 30 citations and is from a domain leading peer-reviewed journal.
(selvanathan2022mitochondrialironsulfurcluster pages 3-4): Arthavan Selvanathan and Bindu Parayil Sankaran. Mitochondrial iron-sulfur cluster biogenesis and neurological disorders. Mitochondrion, 62:41-49, Jan 2022. URL: https://doi.org/10.1016/j.mito.2021.10.004, doi:10.1016/j.mito.2021.10.004. This article has 18 citations and is from a peer-reviewed journal.

Citations

maio2022mammalianironsulfur pages 1-2
nasta2019structuralpropertiesof pages 7-8
maio2020outliningthecomplex pages 10-12
selvanathan2022mitochondrialironsulfurcluster pages 3-4
nasta2019structuralpropertiesof pages 10-11
bargagna2024molecularpathwaysforb pages 16-20
bargagna2024molecularpathwaysfor pages 16-20
4Fe-4S
2Fe-2S
4fe4s
4fe-4s
2fe-2s
https://doi.org/10.1002/iub.2597;
https://doi.org/10.1016/j.tibs.2020.02.001.
https://doi.org/10.1002/humu.23396.
https://doi.org/10.1073/pnas.2003982117.
https://doi.org/10.1038/s41598-019-55313-5.
https://doi.org/10.1016/j.tibs.2020.02.001;
https://doi.org/10.1002/iub.2597.
https://doi.org/10.1002/humu.23396;
https://doi.org/10.3390/biomedicines9080989.
https://doi.org/10.1073/pnas.2003982117;
https://doi.org/10.1038/s41598-019-55313-5
https://doi.org/10.1073/pnas.2003982117
https://doi.org/10.1016/j.tibs.2020.02.001
https://doi.org/10.1002/humu.23396
https://doi.org/10.3390/biomedicines9080989
https://doi.org/10.1002/iub.2597
https://doi.org/10.1016/j.mito.2021.10.004
https://doi.org/10.52601/bpr.2021.200038
https://doi.org/10.1038/s41598-019-55313-5;
https://doi.org/10.3390/biomedicines9080989;
https://doi.org/10.1016/j.tibs.2020.02.001,
https://doi.org/10.1002/humu.23396,
https://doi.org/10.1002/iub.2597,
https://doi.org/10.1073/pnas.2003982117,
https://doi.org/10.1038/s41598-019-55313-5,
https://doi.org/10.1016/j.mito.2021.10.004,

📄 View Raw YAML

id: Q86U28
gene_symbol: ISCA2
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: ISCA2 is a mitochondrial A-type iron-sulfur cluster assembly 
  protein of the HesB/IscA family that functions in the late-stage maturation of
  mitochondrial [4Fe-4S] proteins. It works in concert with ISCA1 and IBA57 to 
  assemble [4Fe-4S] clusters by reductive fusion of two [2Fe-2S] clusters 
  donated by GLRX5. The electron input for this fusion reaction is provided by 
  ferredoxin FDX2 via FDXR. ISCA2 forms homodimers and heterodimers with ISCA1 
  (the ISCA1:ISCA2 complex), and also forms an oxidation-resistant 
  [2Fe-2S]-bridged heterocomplex with IBA57 (the ISCA2:IBA57 complex). Biallelic
  loss-of-function mutations in ISCA2 cause Multiple Mitochondrial Dysfunctions 
  Syndrome type 4 (MMDS4), characterized by early-onset leukodystrophy, 
  hyperglycinemia, impaired protein lipoylation, and mtDNA depletion.
existing_annotations:
  - term:
      id: GO:0005739
      label: mitochondrion
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: ISCA2 is confirmed to localize to mitochondria based on 
        phylogenetic inference (IBA) and multiple experimental studies. The 
        protein functions in the mitochondrial matrix as part of the late-stage 
        ISC assembly pathway (PMID:22323289, PMID:25347204).
      action: ACCEPT
      reason: Mitochondrial localization is well-established for ISCA2. The IBA 
        annotation is consistent with experimental evidence showing ISCA2 
        functions in mitochondrial [4Fe-4S] cluster assembly. Direct 
        experimental evidence (IDA from PMID:22323289) also confirms this 
        localization.
      supported_by:
        - reference_id: PMID:25347204
          supporting_text: The generation of [4Fe-4S] clusters in mitochondria 
            critically depends, in both yeast and human cells, on two A-type ISC
            proteins (in mammals named ISCA1 and ISCA2)
  - term:
      id: GO:0016226
      label: iron-sulfur cluster assembly
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: ISCA2 is directly involved in iron-sulfur cluster assembly, 
        specifically in the late-stage [4Fe-4S] cluster assembly pathway. The 
        IBA annotation appropriately captures this core function 
        (PMID:25347204).
      action: ACCEPT
      reason: While ISCA2's role is specifically in [4Fe-4S] cluster assembly, 
        the general term iron-sulfur cluster assembly is still correct and 
        appropriate. The ISCA1:ISCA2 heterodimeric complex receives [2Fe-2S] 
        clusters from GRX5 and assembles them into [4Fe-4S] clusters 
        (PMID:25347204). The IBA annotation from PANTHER is valid.
      supported_by:
        - reference_id: PMID:25347204
          supporting_text: The generation of [4Fe-4S] clusters in mitochondria 
            critically depends, in both yeast and human cells, on two A-type ISC
            proteins (in mammals named ISCA1 and ISCA2)
        - reference_id: file:human/ISCA2/ISCA2-deep-research-falcon.md
          supporting_text: ISCA2 is a mitochondrial A-type Fe-S assembly factor 
            in the HesB/IscA family. It acts as a late-acting secondary carrier 
            in the ISC pathway
  - term:
      id: GO:0051604
      label: protein maturation
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: ISCA2 contributes to the maturation of mitochondrial [4Fe-4S] 
        proteins by facilitating the assembly and transfer of [4Fe-4S] clusters 
        to apo-proteins including aconitase and lipoic acid synthase 
        (PMID:22323289, PMID:25347204).
      action: ACCEPT
      reason: This annotation correctly captures ISCA2's role in promoting the 
        maturation of [4Fe-4S]-containing proteins. The term is appropriate as 
        ISCA2 is required for the functional maturation of mitochondrial 
        [4Fe-4S] proteins.
      supported_by:
        - reference_id: PMID:25347204
          supporting_text: These findings imply that such heterodimeric complex 
            is the functional unit in mitochondria receiving [2Fe-2S] clusters 
            from hGRX5 and assembling [4Fe-4S] clusters before their transfer to
            the final target apo proteins
  - term:
      id: GO:0005506
      label: iron ion binding
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: ISCA2 binds iron ions as part of its [2Fe-2S] and [4Fe-4S] 
        cluster-binding capacity. The iron binding is integral to its function 
        in Fe-S cluster assembly.
      action: ACCEPT
      reason: Iron ion binding is inherent to ISCA2's function as an Fe-S 
        cluster assembly protein. The protein coordinates iron through conserved
        cysteine residues (Cys79, Cys144, Cys146) as documented in UniProt and 
        structural studies. This is a valid but somewhat generic annotation that
        is subsumed by the more specific cluster binding annotations.
      supported_by:
        - reference_id: PMID:25347204
          supporting_text: ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a 
            dimeric state
  - term:
      id: GO:0051537
      label: 2 iron, 2 sulfur cluster binding
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: ISCA2 binds [2Fe-2S] clusters as part of its role in Fe-S cluster
        assembly. The [2Fe-2S] cluster is received from GLRX5 and is an 
        intermediate in [4Fe-4S] assembly (PMID:25347204, PMID:31831856).
      action: ACCEPT
      reason: '[2Fe-2S] cluster binding by ISCA2 is well-documented. ISCA2 can hold
        a [2Fe-2S] cluster and forms a [2Fe-2S]-bridged heterocomplex with IBA57.
        The cluster is an intermediate received from GLRX5 that is subsequently converted
        to [4Fe-4S].'
      supported_by:
        - reference_id: PMID:25347204
          supporting_text: ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a 
            dimeric state
        - reference_id: PMID:31831856
          supporting_text: The [2Fe-2S] cluster is out of the ISCA2 core while 
            being shared with IBA57 in the dimer
  - term:
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: ISCA2, as part of the ISCA1:ISCA2 heterodimeric complex, binds 
        [4Fe-4S] clusters that are assembled from two [2Fe-2S] precursors 
        (PMID:25347204).
      action: ACCEPT
      reason: '[4Fe-4S] cluster binding is a core function of the ISCA1:ISCA2 complex.
        The heterodimeric complex assembles and transiently holds a [4Fe-4S] cluster
        before transfer to target apo-proteins.'
      supported_by:
        - reference_id: PMID:25347204
          supporting_text: ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a 
            dimeric state
        - reference_id: PMID:25347204
          supporting_text: the two GRX5-donated [2Fe-2S](2+) clusters generate a
            [4Fe-4S](2+) cluster
  - term:
      id: GO:0005739
      label: mitochondrion
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: IEA annotation for mitochondrial localization based on UniProt 
        subcellular location vocabulary. Consistent with experimental evidence.
      action: ACCEPT
      reason: This IEA annotation is consistent with the IBA and IDA evidence 
        for mitochondrial localization. While redundant with higher-quality 
        annotations, it provides a valid automatic annotation that does not 
        conflict with established knowledge.
      supported_by:
        - reference_id: PMID:25347204
          supporting_text: The generation of [4Fe-4S] clusters in mitochondria 
            critically depends, in both yeast and human cells, on two A-type ISC
            proteins (in mammals named ISCA1 and ISCA2)
  - term:
      id: GO:0016226
      label: iron-sulfur cluster assembly
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: IEA annotation for iron-sulfur cluster assembly based on InterPro
        domain mapping.
      action: ACCEPT
      reason: This IEA annotation is correct based on domain analysis 
        (FeS_cluster_insertion domain IPR016092). Consistent with ISCA2's role 
        in Fe-S biogenesis and the IBA annotation for the same term.
      supported_by:
        - reference_id: PMID:25347204
          supporting_text: The generation of [4Fe-4S] clusters in mitochondria 
            critically depends, in both yeast and human cells, on two A-type ISC
            proteins
  - term:
      id: GO:0046872
      label: metal ion binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: IEA annotation for metal ion binding based on UniProt keyword 
        mapping. Very general annotation subsumed by more specific iron and Fe-S
        cluster binding terms.
      action: MARK_AS_OVER_ANNOTATED
      reason: While technically correct (ISCA2 binds iron as part of Fe-S 
        clusters), this term is overly broad and uninformative given the more 
        specific annotations for iron ion binding and Fe-S cluster binding that 
        are already present. It adds little value beyond what is captured by 
        more specific MF terms.
  - term:
      id: GO:0051536
      label: iron-sulfur cluster binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: IEA annotation for general iron-sulfur cluster binding based on 
        combined IEA methods.
      action: ACCEPT
      reason: This general Fe-S cluster binding annotation is correct and serves
        as a parent term encompassing both [2Fe-2S] and [4Fe-4S] cluster 
        binding, which are both relevant to ISCA2 function. More specific child 
        terms are also annotated.
      supported_by:
        - reference_id: PMID:25347204
          supporting_text: ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a 
            dimeric state
  - term:
      id: GO:0120510
      label: mitochondrial [4Fe-4S] assembly complex
    evidence_type: IEA
    original_reference_id: GO_REF:0000117
    review:
      summary: IEA annotation indicating ISCA2 is part of the mitochondrial 
        [4Fe-4S] assembly complex, based on ARBA machine learning.
      action: ACCEPT
      reason: This is an accurate annotation. ISCA2 is indeed a component of the
        mitochondrial [4Fe-4S] assembly complex (ISCA1:ISCA2 complex) as defined
        in GO. The GO term definition explicitly states "In humans it consists 
        of ISCA1 and ISCA2."
      supported_by:
        - reference_id: PMID:25347204
          supporting_text: We found that (i) ISCA2 binds either [2Fe-2S] or 
            [4Fe-4S] cluster in a dimeric state, and (ii) two molecules of 
            [2Fe-2S](2+) GRX5 donate their cluster to a heterodimeric 
            ISCA1/ISCA2 complex
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:25347204
    review:
      summary: IPI annotation for protein binding based on ISCA2 interaction 
        with ISCA1 (Q9BUE6) demonstrated in this study.
      action: MODIFY
      reason: The annotation captures a real interaction (ISCA2 with ISCA1), but
        "protein binding" is uninformative. ISCA2 forms a functional 
        heterodimeric complex with ISCA1 that assembles [4Fe-4S] clusters. This 
        is better captured by the complex membership annotation (GO:0120510) or 
        the identical protein binding annotation for homodimerization.
      proposed_replacement_terms:
        - id: GO:0120510
          label: mitochondrial [4Fe-4S] assembly complex
      supported_by:
        - reference_id: PMID:25347204
          supporting_text: We found that (i) ISCA2 binds either [2Fe-2S] or 
            [4Fe-4S] cluster in a dimeric state, and (ii) two molecules of 
            [2Fe-2S](2+) GRX5 donate their cluster to a heterodimeric 
            ISCA1/ISCA2 complex
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:25416956
    review:
      summary: IPI annotation for protein binding based on high-throughput 
        interactome mapping (interaction with RNF41/Q9H4P4).
      action: MARK_AS_OVER_ANNOTATED
      reason: This annotation derives from high-throughput interactome mapping 
        and captures an interaction with RNF41 (E3 ubiquitin ligase). While the 
        interaction may be real, the generic "protein binding" term is 
        uninformative and the biological relevance of ISCA2-RNF41 interaction to
        ISCA2's core Fe-S assembly function is unclear.
      supported_by:
        - reference_id: PMID:25416956
          supporting_text: A proteome-scale map of the human interactome 
            network.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:31831856
    review:
      summary: IPI annotation for protein binding based on ISCA2-IBA57 
        interaction demonstrated by structural and biophysical studies (Nasta et
        al., 2019).
      action: MODIFY
      reason: This captures the important ISCA2-IBA57 interaction, but "protein 
        binding" is uninformative. ISCA2 forms a [2Fe-2S]-bridged heterocomplex 
        with IBA57 that is structurally characterized and functionally important
        for late-stage Fe-S assembly.
      proposed_replacement_terms:
        - id: GO:0140132
          label: iron-sulfur cluster chaperone activity
      supported_by:
        - reference_id: PMID:31831856
          supporting_text: The [2Fe-2S] cluster is out of the ISCA2 core while 
            being shared with IBA57 in the dimer
        - reference_id: PMID:31831856
          supporting_text: dimeric [2Fe-2S] ISCA2-IBA57 hetero-complex is a 
            physiologically relevant species
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:32296183
    review:
      summary: IPI annotation for multiple protein interactions from 
        high-throughput binary interactome mapping.
      action: MARK_AS_OVER_ANNOTATED
      reason: This is a high-throughput study identifying multiple interactors. 
        The generic "protein binding" term is uninformative. Many of the 
        reported interactors (e.g., SUOX, GEM, EIF3E) lack clear functional 
        relevance to ISCA2's core Fe-S assembly function and may represent 
        experimental artifacts or transient interactions.
      supported_by:
        - reference_id: PMID:32296183
          supporting_text: Apr 8. A reference map of the human binary protein 
            interactome.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:32814053
    review:
      summary: IPI annotation from interactome mapping in the context of 
        neurodegenerative disease protein networks.
      action: MARK_AS_OVER_ANNOTATED
      reason: This high-throughput interactome study reports multiple ISCA2 
        interactors, but the generic "protein binding" annotation is 
        uninformative. The biological relevance of these interactions to ISCA2's
        core Fe-S assembly function is unclear.
      supported_by:
        - reference_id: PMID:32814053
          supporting_text: Interactome Mapping Provides a Network of 
            Neurodegenerative Disease Proteins and Uncovers Widespread Protein 
            Aggregation in Affected Brains.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:33961781
    review:
      summary: IPI annotation from dual proteome-scale network studies showing 
        ISCA2 interactions with IBA57, ISCA1, and RNF41.
      action: MARK_AS_OVER_ANNOTATED
      reason: While this study confirms biologically relevant interactions 
        (ISCA1, IBA57), the generic "protein binding" term is uninformative. The
        relevant functional interactions are better captured by complex 
        membership (GO:0120510) and specific binding annotations.
      supported_by:
        - reference_id: PMID:33961781
          supporting_text: 2021 May 6. Dual proteome-scale networks reveal 
            cell-specific remodeling of the human interactome.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:39408793
    review:
      summary: IPI annotation based on ISCA2-IBA57 interaction studies in 
        context of MMDS3 pathogenic variant analysis.
      action: ACCEPT
      reason: This study specifically characterizes the ISCA2-IBA57 interaction 
        in the context of disease-causing IBA57 variants. While "protein 
        binding" is generic, this annotation has clear functional relevance to 
        understanding ISCA2's role in the late ISC pathway and disease 
        mechanisms.
      supported_by:
        - reference_id: file:human/ISCA2/ISCA2-deep-research-falcon.md
          supporting_text: ISCA2 forms a dimer and assembles a [2Fe-2S] 
            ISCA2-IBA57 heterocomplex that is oxidation-resistant and can 
            reactivate apo-aconitase
        - reference_id: PMID:39408793
          supporting_text: 'Defects in the Maturation of Mitochondrial Iron-Sulfur
            Proteins: Biophysical Investigation of the MMDS3 Causing Gly104Cys Variant
            of IBA57.'
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:40205054
    review:
      summary: IPI annotation from multimodal cell mapping study showing ISCA2 
        interactions.
      action: MARK_AS_OVER_ANNOTATED
      reason: High-throughput study with generic "protein binding" annotation 
        that is uninformative about ISCA2's specific molecular function.
      supported_by:
        - reference_id: PMID:40205054
          supporting_text: Apr 9. Multimodal cell maps as a foundation for 
            structural and functional genomics.
  - term:
      id: GO:0042802
      label: identical protein binding
    evidence_type: IPI
    original_reference_id: PMID:25347204
    review:
      summary: ISCA2 forms homodimers, as demonstrated in structural and 
        biochemical studies (PMID:25347204, PMID:31831856).
      action: ACCEPT
      reason: ISCA2 homodimerization is well-documented and functionally 
        relevant. The apo form of ISCA2 is dimeric, and this dimerization is 
        important for its cluster binding and assembly function.
      supported_by:
        - reference_id: PMID:25347204
          supporting_text: ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a 
            dimeric state
        - reference_id: PMID:31831856
          supporting_text: ISCA2-IBA57 complex with ISCA2 providing the 
            homodimerization core interface
  - term:
      id: GO:0042802
      label: identical protein binding
    evidence_type: IPI
    original_reference_id: PMID:31831856
    review:
      summary: Structural study (SAXS and modeling) confirming ISCA2 
        homodimerization as the core interface in the ISCA2-IBA57 complex.
      action: ACCEPT
      reason: This study provides structural evidence for ISCA2 
        homodimerization. The ISCA2 dimer provides the core interface for 
        complex formation with IBA57.
      supported_by:
        - reference_id: PMID:31831856
          supporting_text: ISCA2-IBA57 complex with ISCA2 providing the 
            homodimerization core interface
  - term:
      id: GO:0005739
      label: mitochondrion
    evidence_type: IDA
    original_reference_id: PMID:22323289
    review:
      summary: Direct experimental evidence (IDA) for mitochondrial localization
        from the foundational study establishing ISCA2's role in [4Fe-4S] 
        protein maturation.
      action: ACCEPT
      reason: This is high-quality experimental evidence for mitochondrial 
        localization from the key study by Sheftel et al. that established the 
        function of human ISCA1, ISCA2, and IBA57 in [4Fe-4S] protein 
        maturation.
      supported_by:
        - reference_id: file:human/ISCA2/ISCA2-deep-research-falcon.md
          supporting_text: ISCA2 functions in the mitochondrial matrix, 
            evidenced by its role in mitochondrial [4Fe-4S] client maturation
        - reference_id: PMID:22323289
          supporting_text: Feb 9. The human mitochondrial ISCA1, ISCA2, and 
            IBA57 proteins are required for [4Fe-4S] protein maturation.
  - term:
      id: GO:0051604
      label: protein maturation
    evidence_type: IDA
    original_reference_id: PMID:25347204
    review:
      summary: Direct experimental evidence that ISCA2 is involved in [4Fe-4S] 
        protein maturation by assembling clusters for transfer to target 
        apo-proteins.
      action: ACCEPT
      reason: This annotation is based on biochemical reconstitution studies 
        showing the ISCA1:ISCA2 complex assembles [4Fe-4S] clusters for transfer
        to target proteins.
      supported_by:
        - reference_id: PMID:25347204
          supporting_text: These findings imply that such heterodimeric complex 
            is the functional unit in mitochondria receiving [2Fe-2S] clusters 
            from hGRX5 and assembling [4Fe-4S] clusters before their transfer to
            the final target apo proteins
  - term:
      id: GO:0051604
      label: protein maturation
    evidence_type: NAS
    original_reference_id: PMID:31831856
    review:
      summary: Non-traceable author statement annotation for protein maturation 
        function based on the ISCA2-IBA57 structural study.
      action: ACCEPT
      reason: While NAS is a weaker evidence code, the annotation is consistent 
        with the well-established role of ISCA2 in [4Fe-4S] protein maturation. 
        The referenced paper provides structural context for understanding how 
        ISCA2 contributes to this process.
      supported_by:
        - reference_id: PMID:31831856
          supporting_text: dimeric [2Fe-2S] ISCA2-IBA57 hetero-complex is a 
            physiologically relevant species
  - term:
      id: GO:0005739
      label: mitochondrion
    evidence_type: HTP
    original_reference_id: PMID:34800366
    review:
      summary: High-throughput proteomics study confirming ISCA2 as part of the 
        high-confidence mitochondrial proteome.
      action: ACCEPT
      reason: This high-quality proteomics study provides additional support for
        mitochondrial localization, consistent with other experimental evidence.
      supported_by:
        - reference_id: PMID:34800366
          supporting_text: Epub 2021 Nov 19. Quantitative high-confidence human 
            mitochondrial proteome and its dynamics in cellular context.
  - term:
      id: GO:0120510
      label: mitochondrial [4Fe-4S] assembly complex
    evidence_type: IDA
    original_reference_id: PMID:25347204
    review:
      summary: Direct experimental evidence that ISCA2 is part of the 
        mitochondrial [4Fe-4S] assembly complex (ISCA1:ISCA2 heterodimer) that 
        assembles [4Fe-4S] clusters.
      action: ACCEPT
      reason: This is a key annotation capturing ISCA2's core function. The 
        study demonstrates that the ISCA1:ISCA2 heterodimeric complex is the 
        functional unit for [4Fe-4S] cluster assembly.
      supported_by:
        - reference_id: PMID:25347204
          supporting_text: We found that (i) ISCA2 binds either [2Fe-2S] or 
            [4Fe-4S] cluster in a dimeric state, and (ii) two molecules of 
            [2Fe-2S](2+) GRX5 donate their cluster to a heterodimeric 
            ISCA1/ISCA2 complex
  - term:
      id: GO:0005759
      label: mitochondrial matrix
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-8878815
    review:
      summary: Reactome pathway annotation indicating ISCA2 functions in the 
        mitochondrial matrix, where [4Fe-4S] cluster formation occurs on the 
        ISCA1:ISCA2 complex.
      action: ACCEPT
      reason: The mitochondrial matrix localization is consistent with ISCA2's 
        role in late-stage Fe-S cluster assembly, which occurs in the matrix 
        compartment. Reactome provides curated pathway context.
      supported_by:
        - reference_id: Reactome:R-HSA-8878815
          supporting_text: Formation of 4Fe-4S cluster on ISCA1:ISCA2
  - term:
      id: GO:0005759
      label: mitochondrial matrix
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-9854984
    review:
      summary: Reactome annotation for mitochondrial matrix localization in 
        context of Fe-S cluster transfer to SDHB.
      action: ACCEPT
      reason: Consistent with ISCA2's role in maturation of mitochondrial 
        [4Fe-4S] proteins including succinate dehydrogenase complex subunits.
      supported_by:
        - reference_id: Reactome:R-HSA-9854984
          supporting_text: Transfer of Fe-S clusters to SDHB
  - term:
      id: GO:0044572
      label: '[4Fe-4S] cluster assembly'
    evidence_type: IDA
    original_reference_id: PMID:25347204
    review:
      summary: 'NEW ANNOTATION: ISCA2 is involved in [4Fe-4S] cluster assembly as
        a biological process. The ISCA1:ISCA2 complex assembles [4Fe-4S] clusters
        from [2Fe-2S] precursors.'
      action: NEW
      reason: The existing annotations include the general term GO:0016226 
        (iron-sulfur cluster assembly), but ISCA2's specific function is 
        [4Fe-4S] cluster assembly, which is captured by the more precise child 
        term GO:0044572.
      supported_by:
        - reference_id: PMID:25347204
          supporting_text: This complex acts as an "assembler" of [4Fe-4S] 
            clusters; i.e., the two GRX5-donated [2Fe-2S](2+) clusters generate 
            a [4Fe-4S](2+) cluster
references:
  - id: GO_REF:0000002
    title: Gene Ontology annotation through association of InterPro records with
      GO terms
    findings: []
  - id: GO_REF:0000033
    title: Annotation inferences using phylogenetic trees
    findings: []
  - id: GO_REF:0000043
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword 
      mapping
    findings: []
  - id: GO_REF:0000044
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular 
      Location vocabulary mapping
    findings: []
  - id: GO_REF:0000117
    title: Electronic Gene Ontology annotations created by ARBA machine learning
      models
    findings: []
  - id: GO_REF:0000120
    title: Combined Automated Annotation using Multiple IEA Methods
    findings: []
  - id: PMID:22323289
    title: The human mitochondrial ISCA1, ISCA2, and IBA57 proteins are required
      for [4Fe-4S] protein maturation.
    findings:
      - statement: Established that ISCA1, ISCA2, and IBA57 are required for 
          mitochondrial [4Fe-4S] protein maturation
        supporting_text: The human mitochondrial ISCA1, ISCA2, and IBA57 
          proteins are required for [4Fe-4S] protein maturation
      - statement: RNAi depletion causes loss of [4Fe-4S] enzyme activities 
          (aconitase, lipoic acid synthase)
        supporting_text: The activities of mitochondrial [4Fe-4S] proteins, 
          including aconitase, respiratory complex I, and lipoic acid synthase, 
          were diminished following depletion of the three proteins
      - statement: Confirmed mitochondrial localization of ISCA2
        supporting_text: We conclude that all three ISC proteins are located in 
          mitochondria
  - id: PMID:25347204
    title: Formation of [4Fe-4S] clusters in the mitochondrial iron-sulfur 
      cluster assembly machinery.
    findings:
      - statement: ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a dimeric 
          state
        supporting_text: ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a 
          dimeric state
      - statement: ISCA1:ISCA2 heterodimeric complex receives [2Fe-2S] clusters 
          from GRX5
        supporting_text: two molecules of [2Fe-2S](2+) GRX5 donate their cluster
          to a heterodimeric ISCA1/ISCA2 complex
      - statement: The complex assembles [4Fe-4S] clusters from two [2Fe-2S] 
          precursors
        supporting_text: the two GRX5-donated [2Fe-2S](2+) clusters generate a 
          [4Fe-4S](2+) cluster
      - statement: Established the ISCA1:ISCA2 complex as the functional unit 
          for [4Fe-4S] assembly
        supporting_text: These findings imply that such heterodimeric complex is
          the functional unit in mitochondria
  - id: PMID:25416956
    title: A proteome-scale map of the human interactome network.
    findings:
      - statement: High-throughput interactome mapping identified ISCA2 protein 
          interactions
  - id: PMID:31831856
    title: 'Structural properties of [2Fe-2S] ISCA2-IBA57: a complex of the mitochondrial
      iron-sulfur cluster assembly machinery.'
    findings:
      - statement: ISCA2 forms homodimer that provides core interface for IBA57 
          interaction
        supporting_text: ISCA2-IBA57 complex with ISCA2 providing the 
          homodimerization core interface
      - statement: Characterized [2Fe-2S]-bridged ISCA2-IBA57 heterocomplex 
          structure by SAXS
        supporting_text: The [2Fe-2S] cluster is out of the ISCA2 core while 
          being shared with IBA57 in the dimer
      - statement: Complex forms dimer of dimers (heterotetramer)
        supporting_text: dimeric [2Fe-2S] ISCA2-IBA57 hetero-complex is a 
          physiologically relevant species
      - statement: Defined molecular basis for pathogenic IBA57 Arg146Trp 
          mutation
        supporting_text: The specific interaction pattern identified from the 
          dimeric [2Fe-2S]2+ ISCA2-IBA57 structural model allowed us to define 
          the molecular grounds of the pathogenic Arg146Trp mutation of IBA57
  - id: PMID:32296183
    title: A reference map of the human binary protein interactome.
    findings:
      - statement: High-throughput binary interactome mapping
  - id: PMID:32814053
    title: Interactome Mapping Provides a Network of Neurodegenerative Disease 
      Proteins.
    findings:
      - statement: ISCA2 interactors identified in neurodegenerative disease 
          protein network context
  - id: PMID:33961781
    title: Dual proteome-scale networks reveal cell-specific remodeling of the 
      human interactome.
    findings:
      - statement: Confirmed ISCA2 interactions with ISCA1 and IBA57
  - id: PMID:34800366
    title: Quantitative high-confidence human mitochondrial proteome and its 
      dynamics in cellular context.
    findings:
      - statement: ISCA2 identified as high-confidence mitochondrial protein
  - id: PMID:39408793
    title: 'Defects in the Maturation of Mitochondrial Iron-Sulfur Proteins: Biophysical
      Investigation of the MMDS3 Causing Gly104Cys Variant of IBA57.'
    findings:
      - statement: Characterization of ISCA2-IBA57 interaction in context of 
          disease variants
  - id: PMID:40205054
    title: Multimodal cell maps as a foundation for structural and functional 
      genomics.
    findings:
      - statement: ISCA2 protein interactions from multimodal cell mapping
  - id: Reactome:R-HSA-8878815
    title: Formation of 4Fe-4S cluster on ISCA1:ISCA2
    findings:
      - statement: Pathway curation placing ISCA2 in [4Fe-4S] cluster formation 
          reaction
  - id: Reactome:R-HSA-9854984
    title: Transfer of Fe-S clusters to SDHB
    findings:
      - statement: ISCA2 involved in pathway for Fe-S cluster transfer to 
          respiratory chain components
core_functions:
  - description: ISCA2 is a core component of the late-stage mitochondrial ISC 
      pathway, functioning specifically in [4Fe-4S] cluster assembly. 
      Biochemical reconstitution studies (PMID:25347204) demonstrated that the 
      ISCA1:ISCA2 heterodimeric complex receives [2Fe-2S] clusters from GLRX5 
      and assembles them into [4Fe-4S] clusters through reductive fusion, with 
      electrons supplied by FDX2/FDXR.
    molecular_function:
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
    directly_involved_in:
      - id: GO:0044572
        label: '[4Fe-4S] cluster assembly'
      - id: GO:0051604
        label: protein maturation
    locations:
      - id: GO:0005759
        label: mitochondrial matrix
    in_complex:
      id: GO:0120510
      label: mitochondrial [4Fe-4S] assembly complex
    supported_by:
      - reference_id: PMID:25347204
        supporting_text: This complex acts as an "assembler" of [4Fe-4S] 
          clusters; i.e., the two GRX5-donated [2Fe-2S](2+) clusters generate a 
          [4Fe-4S](2+) cluster
      - reference_id: file:human/ISCA2/ISCA2-deep-research-falcon.md
        supporting_text: ISCA2 is a mitochondrial A-type Fe-S assembly factor in
          the HesB/IscA family. It acts as a late-acting secondary carrier in 
          the ISC pathway
tags:
  - iron-sulfur-cluster-biogenesis

ISCA2

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Gene Research for Functional Annotation

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