ACADM encodes mitochondrial medium-chain acyl-CoA dehydrogenase (MCAD), a soluble matrix flavoenzyme that catalyzes the initial dehydrogenation step of fatty acid beta-oxidation. The mature homotetramer contains one FAD per subunit and converts acyl-CoA substrates to trans-2-enoyl-CoA, transferring electrons to electron transfer flavoprotein (ETF). Its preferred substrates have medium-length chains, with maximal activity near C6-C8; its substrate range also includes shorter and longer chains. This activity supports energy production from fat, especially during fasting. Biallelic loss-of-function variants cause MCAD deficiency, with impaired tolerance of catabolic stress; many missense variants disrupt protein folding, stability, or tetramer assembly.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | MODIFY | Summary: The PAINT cytoplasm annotation is compatible with mitochondrial residence, but the target-specific matrix location is more informative. Reason: Refine to mitochondrial matrix using human fractionation evidence in PMID:16020546 and the curated UniProt location. Cytoplasm is broad, not a false location; no loss of ancestral function or defective PAINT node placement is inferred. Propagation Review Root cause: TERM SCOPING PROBLEM Sources checked: PANTHER:PTN002535634 SUPPORTS TRANSFER PAINT ancestral node PTN002535634 supplies this cytoplasm inference. Independent human localization/catalysis supports the relevant biology; the full tree and IBD placement were not reconstructed. Human self-inclusion in descendant evidence is legitimate, not circular. Proposed replacements: mitochondrial matrix Supporting Evidence: PMID:1902818 Demonstration of intra-mitochondrial mature MCAD indistinguishable in size (42.5-kDa) from control MCAD |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT evidence places ACADM in mitochondria, the organelle where its core catalytic activity occurs. Reason: The broad location accurately describes a core compartment. The more precise matrix annotation does not make mitochondrial residence a peripheral function. Independent human evidence corroborates the inference. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000098033 SUPPORTS TRANSFER PAINT ancestral node PTN000098033 supplies this mitochondrion inference. Independent human localization/catalysis supports the relevant biology; the full tree and IBD placement were not reconstructed. Human self-inclusion in descendant evidence is legitimate, not circular. Supporting Evidence: PMID:1902818 Demonstration of intra-mitochondrial mature MCAD indistinguishable in size (42.5-kDa) from control MCAD |
| GO:0051793 medium-chain fatty acid catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically inferred role in medium-chain fatty acid catabolism, directly matching MCAD's biochemical function. This is a core process for MCAD and is also independently supported by direct experimental annotations (PMID:1970566). Reason: MCAD catabolizes medium-chain fatty acids via beta-oxidation; this term accurately captures its core biological process. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000098033 SUPPORTS TRANSFER PAINT ancestral node PTN000098033 supplies this medium-chain fatty acid catabolic process inference. Independent human localization/catalysis supports the relevant biology; the full tree and IBD placement were not reconstructed. Human self-inclusion in descendant evidence is legitimate, not circular. Supporting Evidence: PMID:19224950 MCAD is a member of the acyl-CoA dehydrogenase (ACAD) family of flavoproteins, which catalyzes the first step of the mitochondrial Ξ²-oxidation of medium-chain fatty acids |
| GO:0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically inferred participation in the acyl-CoA-dehydrogenase-dependent step of beta-oxidation. This is the defining process for ACAD-family enzymes and is the most precise process term for MCAD's role, strongly supported by direct experimental annotations. Reason: MCAD performs the acyl-CoA dehydrogenase step of beta-oxidation; this is a core process annotation. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN002535634 SUPPORTS TRANSFER PAINT ancestral node PTN002535634 supplies this fatty acid beta-oxidation using acyl-CoA dehydrogenase inference. Independent human localization/catalysis supports the relevant biology; the full tree and IBD placement were not reconstructed. Human self-inclusion in descendant evidence is legitimate, not circular. Supporting Evidence: PMID:19224950 MCAD is a member of the acyl-CoA dehydrogenase (ACAD) family of flavoproteins, which catalyzes the first step of the mitochondrial Ξ²-oxidation of medium-chain fatty acids |
| GO:0070991 medium-chain fatty acyl-CoA dehydrogenase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically inferred medium-chain acyl-CoA dehydrogenase activity. This is MCAD's defining molecular function and is independently and directly supported by enzyme characterization (PMID:8823175, PMID:21237683, PMID:1970566). The IBA call is at the correct level of specificity. Reason: This is the core molecular function of MCAD, corroborated by multiple direct biochemical studies establishing optimal activity toward medium-chain (C6-C8) acyl-CoA substrates. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000098033 SUPPORTS TRANSFER PAINT ancestral node PTN000098033 supplies this medium-chain fatty acyl-CoA dehydrogenase activity inference. Independent human localization/catalysis supports the relevant biology; the full tree and IBD placement were not reconstructed. Human self-inclusion in descendant evidence is legitimate, not circular. Supporting Evidence: PMID:3597357 The products of SCA dehydrogenase/butyryl-CoA, MCA dehydrogenase/octanoyl-CoA, and IV dehydrogenase/isovaleryl-CoA reactions were identified as crotonyl-CoA, 2-octenoyl-CoA, and 3-methylcrotonyl-CoA |
| GO:0003995 acyl-CoA dehydrogenase activity | IEA GO_REF:0000120 | ACCEPT | Summary: ACADM has acyl-CoA dehydrogenase activity, as demonstrated by its FAD-dependent acyl-CoA dehydrogenation. Reason: This broader catalytic class correctly describes the same core reaction as the medium-chain child term. Breadth alone does not make a core enzyme activity non-core. Propagation Review Root cause: NO FAILURE CORE Sources checked: ARBA:ARBA00026877 UNRESOLVED The proximate ARBA rule is identified, but its predicates and training evidence were not inspected. The annotation judgment uses independent human biochemical or localization evidence, not a claim that the rule internals were validated. InterPro:IPR006089 SUPPORTS TRANSFER This domain/site is listed in the cached UniProt ACAD-family architecture. It is compatible with the assigned broad chemistry or cofactor binding; direct human experiments, not domain presence alone, establish activity. The underlying InterPro2GO rule was not separately re-derived. Supporting Evidence: PMID:3597357 The products of SCA dehydrogenase/butyryl-CoA, MCA dehydrogenase/octanoyl-CoA, and IV dehydrogenase/isovaleryl-CoA reactions were identified as crotonyl-CoA, 2-octenoyl-CoA, and 3-methylcrotonyl-CoA |
| GO:0004466 long-chain fatty acyl-CoA dehydrogenase activity | IEA GO_REF:0000116 | KEEP AS NON CORE | Summary: The Rhea mappings describe ACADM dehydrogenation of C14 and C16 acyl-CoAs, within the GO long-chain category. Reason: The cached UniProt record explicitly assigns the C14 and C16 reactions to human MCAD, citing PMID:21237683 and PMID:8823175. A medium-chain optimum does not exclude these activities; the GO term describes catalysis, not exclusive substrate preference. Retain the broader substrate capacity as non-core without claiming a major physiological long-chain role. The earlier high-Km assertion is withdrawn: the curated record lists lower Km values for C14/C16 than C8, and Km alone is not catalytic efficiency. The original full kinetic panel was not re-extracted. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: RHEA:43448 SUPPORTS TRANSFER The cached human UniProt catalytic record explicitly lists RHEA:43448 for C16 acyl-CoA dehydrogenation with primary literature provenance. Retain as secondary substrate capacity; no exclusive specificity is asserted. RHEA:47316 SUPPORTS TRANSFER The cached human UniProt catalytic record explicitly lists RHEA:47316 for C14 acyl-CoA dehydrogenation with primary literature provenance. Retain as secondary substrate capacity; no exclusive specificity is asserted. Supporting Evidence: file:human/ACADM/ACADM-uniprot.txt chains such as C14 and C16 PMID:8823175 native MCADH (hexanoyl/octanoyl-CoA) |
| GO:0005739 mitochondrion | IEA GO_REF:0000120 | ACCEPT | Summary: Combined electronic evidence places ACADM in mitochondria, the organelle where its core catalytic activity occurs. Reason: The broad location accurately describes a core compartment. The more precise matrix annotation does not make mitochondrial residence a peripheral function. Independent human evidence corroborates the inference. Propagation Review Root cause: NO FAILURE CORE Sources checked: ARBA:ARBA00026962 UNRESOLVED The proximate ARBA rule is identified, but its predicates and training evidence were not inspected. The annotation judgment uses independent human biochemical or localization evidence, not a claim that the rule internals were validated. UniProtKB:P45952 UNRESOLVED Mouse Acadm donor identity is verified. The historical MGI graph lists multiple mitochondrial-localization sources, but the exact evidence selected by this Ensembl transfer was not isolated. Independent human protein localization supports the target judgment. ensembl:ENSMUSP00000072483 UNRESOLVED Mouse Acadm donor identity is verified. The historical MGI graph lists multiple mitochondrial-localization sources, but the exact evidence selected by this Ensembl transfer was not isolated. Independent human protein localization supports the target judgment. InterPro:IPR034180 SUPPORTS TRANSFER The cached UniProt record identifies IPR034180 as MCAD, consistent with the directly assayed medium-chain enzyme and mitochondrial beta-oxidation. Supporting Evidence: PMID:1902818 Demonstration of intra-mitochondrial mature MCAD indistinguishable in size (42.5-kDa) from control MCAD |
| GO:0005759 mitochondrial matrix | IEA GO_REF:0000044 | ACCEPT | Summary: Automated subcellular-location-based annotation to mitochondrial matrix, matching the experimentally supported localization of this soluble matrix flavoenzyme. This is the core location annotation for MCAD. Reason: MCAD is a soluble mitochondrial matrix protein; matrix is the correct, precise compartment. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB-SubCell:SL-0170 SUPPORTS TRANSFER SL-0170 maps the explicit UniProt mitochondrial matrix location, corroborated by MCAD fractionation in the full primary PMID:16020546. Supporting Evidence: file:human/ACADM/ACADM-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix |
| GO:0006635 fatty acid beta-oxidation | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based annotation to fatty acid beta-oxidation, the pathway in which MCAD catalyzes the initial dehydrogenation. The process is supported by purified human enzyme studies and disease genetics. Reason: MCAD catalyzes the first step of mitochondrial fatty acid beta-oxidation; this is a core process annotation. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR034180 SUPPORTS TRANSFER The cached UniProt record identifies IPR034180 as MCAD, consistent with the directly assayed medium-chain enzyme and mitochondrial beta-oxidation. Supporting Evidence: PMID:19224950 catalyzes the first step of the mitochondrial Ξ²-oxidation of medium-chain fatty acids |
| GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors | IEA GO_REF:0000002 | ACCEPT | Summary: ACADM has oxidoreductase activity, acting on the CH-CH group of donors, as demonstrated by its FAD-dependent acyl-CoA dehydrogenation. Reason: This broader catalytic class correctly describes the same core reaction as the medium-chain child term. Breadth alone does not make a core enzyme activity non-core. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR006091 SUPPORTS TRANSFER This domain/site is listed in the cached UniProt ACAD-family architecture. It is compatible with the assigned broad chemistry or cofactor binding; direct human experiments, not domain presence alone, establish activity. The underlying InterPro2GO rule was not separately re-derived. InterPro:IPR009075 SUPPORTS TRANSFER This domain/site is listed in the cached UniProt ACAD-family architecture. It is compatible with the assigned broad chemistry or cofactor binding; direct human experiments, not domain presence alone, establish activity. The underlying InterPro2GO rule was not separately re-derived. InterPro:IPR009100 SUPPORTS TRANSFER This domain/site is listed in the cached UniProt ACAD-family architecture. It is compatible with the assigned broad chemistry or cofactor binding; direct human experiments, not domain presence alone, establish activity. The underlying InterPro2GO rule was not separately re-derived. InterPro:IPR013786 SUPPORTS TRANSFER This domain/site is listed in the cached UniProt ACAD-family architecture. It is compatible with the assigned broad chemistry or cofactor binding; direct human experiments, not domain presence alone, establish activity. The underlying InterPro2GO rule was not separately re-derived. InterPro:IPR036250 SUPPORTS TRANSFER This domain/site is listed in the cached UniProt ACAD-family architecture. It is compatible with the assigned broad chemistry or cofactor binding; direct human experiments, not domain presence alone, establish activity. The underlying InterPro2GO rule was not separately re-derived. InterPro:IPR037069 SUPPORTS TRANSFER This domain/site is listed in the cached UniProt ACAD-family architecture. It is compatible with the assigned broad chemistry or cofactor binding; direct human experiments, not domain presence alone, establish activity. The underlying InterPro2GO rule was not separately re-derived. InterPro:IPR046373 SUPPORTS TRANSFER This domain/site is listed in the cached UniProt ACAD-family architecture. It is compatible with the assigned broad chemistry or cofactor binding; direct human experiments, not domain presence alone, establish activity. The underlying InterPro2GO rule was not separately re-derived. Supporting Evidence: PMID:3597357 The products of SCA dehydrogenase/butyryl-CoA, MCA dehydrogenase/octanoyl-CoA, and IV dehydrogenase/isovaleryl-CoA reactions were identified as crotonyl-CoA, 2-octenoyl-CoA, and 3-methylcrotonyl-CoA |
| GO:0016937 short-chain fatty acyl-CoA dehydrogenase activity | IEA GO_REF:0000116 | KEEP AS NON CORE | Summary: RHEA:43456 records pentanoyl-CoA dehydrogenation, a short-chain reaction compatible with MCAD substrate overlap. Reason: GO:0016937 includes short-chain acyl-CoAs with fewer than six carbons; it is not reserved for the protein named SCAD. Human UniProt assigns the C5 reaction by similarity to rat Acadm P08503. Retain this curated secondary activity with that limitation rather than labeling it false because C6/C8 are preferred. Butyryl-CoA Km is not a measurement of pentanoyl-CoA turnover; no human C5 kinetic measurement is claimed. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: RHEA:43456 SUPPORTS TRANSFER RHEA:43456 is pentanoyl-CoA dehydrogenation in the cached human UniProt record, transferred by similarity from rat Acadm P08503. The rat identity is verified; its underlying C5 experiment was not separately recovered. Supporting Evidence: file:human/ACADM/ACADM-uniprot.txt Xref=Rhea:RHEA:43456 |
| GO:0050660 flavin adenine dinucleotide binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based annotation of FAD binding. MCAD is a flavoprotein carrying one non-covalently bound FAD per subunit, essential for catalysis; the wild-type enzyme is yellow due to its stoichiometric FAD content. This is a correct and supported cofactor-binding function. Reason: FAD binding is experimentally established and required for MCAD catalysis. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR013786 SUPPORTS TRANSFER This domain/site is listed in the cached UniProt ACAD-family architecture. It is compatible with the assigned broad chemistry or cofactor binding; direct human experiments, not domain presence alone, establish activity. The underlying InterPro2GO rule was not separately re-derived. InterPro:IPR037069 SUPPORTS TRANSFER This domain/site is listed in the cached UniProt ACAD-family architecture. It is compatible with the assigned broad chemistry or cofactor binding; direct human experiments, not domain presence alone, establish activity. The underlying InterPro2GO rule was not separately re-derived. Supporting Evidence: PMID:1970566 The wild-type enzyme is a yellow protein due to the content of stoichiometric FAD |
| GO:0070991 medium-chain fatty acyl-CoA dehydrogenase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Automated annotation of the core medium-chain acyl-CoA dehydrogenase activity, fully consistent with the direct experimental (EXP/IDA) annotations. Correct and at the right specificity. Reason: Core molecular function of MCAD, redundantly and directly supported. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P45952 SUPPORTS TRANSFER Mouse Acadm donor identity is verified. The historical MGI comparative graph (2023-03-10) lists this term with IMP evidence from PMID:18459129; the exact current Ensembl transfer record was not re-extracted. Conserved MCAD chemistry and independent human enzyme assays support the target annotation. ensembl:ENSMUSP00000072483 SUPPORTS TRANSFER Mouse Acadm donor identity is verified. The historical MGI comparative graph (2023-03-10) lists this term with IMP evidence from PMID:18459129; the exact current Ensembl transfer record was not re-extracted. Conserved MCAD chemistry and independent human enzyme assays support the target annotation. InterPro:IPR034180 SUPPORTS TRANSFER The cached UniProt record identifies IPR034180 as MCAD, consistent with the directly assayed medium-chain enzyme and mitochondrial beta-oxidation. RHEA:14477 SUPPORTS TRANSFER The cached UniProt catalytic record lists RHEA:14477 within the medium-chain activity and C6/C8/C10/C12 reaction series, supported by the cited human enzyme studies. RHEA:43464 SUPPORTS TRANSFER The cached UniProt catalytic record lists RHEA:43464 within the medium-chain activity and C6/C8/C10/C12 reaction series, supported by the cited human enzyme studies. RHEA:47296 SUPPORTS TRANSFER The cached UniProt catalytic record lists RHEA:47296 within the medium-chain activity and C6/C8/C10/C12 reaction series, supported by the cited human enzyme studies. RHEA:48176 SUPPORTS TRANSFER The cached UniProt catalytic record lists RHEA:48176 within the medium-chain activity and C6/C8/C10/C12 reaction series, supported by the cited human enzyme studies. RHEA:48180 SUPPORTS TRANSFER The cached UniProt catalytic record lists RHEA:48180 within the medium-chain activity and C6/C8/C10/C12 reaction series, supported by the cited human enzyme studies. EC:1.3.8.7 SUPPORTS TRANSFER EC:1.3.8.7 is the medium-chain acyl-CoA dehydrogenase activity assigned in the curated catalytic record and supported by purified human enzyme. Supporting Evidence: PMID:3597357 The products of SCA dehydrogenase/butyryl-CoA, MCA dehydrogenase/octanoyl-CoA, and IV dehydrogenase/isovaleryl-CoA reactions were identified as crotonyl-CoA, 2-octenoyl-CoA, and 3-methylcrotonyl-CoA |
| GO:0005978 glycogen biosynthetic process | IEA GO_REF:0000107 | REMOVE | Summary: Mouse MCAD deficiency changes hepatic glucose-6-phosphate partitioning toward glycogen under fasting and inflammatory stress. Reason: The 2023-03-10 MGI comparative GO graph explicitly traces mouse Acadm (MGI:87867; UniProtKB:P45952) to an IMP annotation from PMID:18459129 / MGI:4412440. This resolves the historical source chain, without claiming the graph is a current GOA snapshot. The primary abstract reports increased allocation of newly formed G6P to glycogen, not an ACADM-catalyzed glycogen-forming step. The independent reviewer inspected the corresponding methods/results in the author thesis chapter; the discussion was not recovered. The observed metabolic coupling is real, but assigning participation in glycogen biosynthesis assigns an unsupported process role to this fatty-acid oxidation enzyme. Remove this electronic process assignment because metabolic coupling does not show that ACADM performs a glycogen-forming step. No claim of an erroneous ortholog identity or fabricated donor annotation is made. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION Sources checked: UniProtKB:P45952 SOURCE WEAK OR INFERRED The identified mouse Acadm donor has a historical IMP glycogen-biosynthesis annotation from PMID:18459129. The source measures glucose flux repartitioning after MCAD loss, providing weak evidence for assigning the enzyme itself to glycogen formation; this is a process-role issue, not an orthology error. ensembl:ENSMUSP00000072483 SOURCE WEAK OR INFERRED The identified mouse Acadm donor has a historical IMP glycogen-biosynthesis annotation from PMID:18459129. The source measures glucose flux repartitioning after MCAD loss, providing weak evidence for assigning the enzyme itself to glycogen formation; this is a process-role issue, not an orthology error. |
| GO:0006111 regulation of gluconeogenesis | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Mouse MCAD deficiency alters gluconeogenic flux specifically during the LPS-induced acute phase response. Reason: The 2023-03-10 MGI comparative GO graph explicitly traces mouse Acadm (MGI:87867; UniProtKB:P45952) to an IMP annotation from PMID:18459129 / MGI:4412440. This resolves the historical source chain, without claiming the graph is a current GOA snapshot. Quantitative flux measurements in the primary abstract show about 20% lower de novo G6P synthesis during the acute phase response, with no reduction during fasting alone. Retain a contextual contribution to regulation of gluconeogenesis through metabolic coupling, rather than a second core enzyme function or a claim of direct transcriptional regulation. The experiment is mouse liver under defined metabolic stress; it does not establish constitutive control in every human tissue. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:P45952 SUPPORTS TRANSFER The historical MGI donor annotation traces to PMID:18459129 and context-dependent hepatic gluconeogenic flux changes. This supports a secondary metabolic regulatory role with the mouse LPS-stress limitation retained. ensembl:ENSMUSP00000072483 SUPPORTS TRANSFER The historical MGI donor annotation traces to PMID:18459129 and context-dependent hepatic gluconeogenic flux changes. This supports a secondary metabolic regulatory role with the mouse LPS-stress limitation retained. |
| GO:0019254 carnitine metabolic process, CoA-linked | IEA GO_REF:0000107 | UNDECIDED | Summary: The carnitine-process donor is identified, but measured acylcarnitine changes do not yet resolve the precise process role. Reason: The 2023-03-10 MGI comparative GO graph explicitly traces mouse Acadm (MGI:87867; UniProtKB:P45952) to an IMP annotation from PMID:18459129 / MGI:4412440. This resolves the historical source chain, without claiming the graph is a current GOA snapshot. The independent reviewer could inspect thesis methods/results reporting tandem-MS carnitine/acylcarnitine measurements and altered medium-chain acylcarnitine pools. The full discussion and a direct mechanism linking ACADM activity to the CoA-linked carnitine process were not recovered. The source citation is no longer missing, but whether this annotation represents process participation or downstream metabolite handling remains unresolved; no absence of such a mechanism from the unread text is asserted. Propagation Review Root cause: UNRESOLVED Sources checked: UniProtKB:P45952 UNRESOLVED The historical MGI donor annotation traces to PMID:18459129. Its carnitine-pool measurements are identified, but precise mechanistic participation could not be resolved from the accessible portions; source identity is resolved, scientific scope remains uncertain. ensembl:ENSMUSP00000072483 UNRESOLVED The historical MGI donor annotation traces to PMID:18459129. Its carnitine-pool measurements are identified, but precise mechanistic participation could not be resolved from the accessible portions; source identity is resolved, scientific scope remains uncertain. |
| GO:0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase | IEA GO_REF:0000120 | ACCEPT | Summary: Automated annotation duplicating the core acyl-CoA-dehydrogenase-dependent beta-oxidation process, consistent with the IBA and direct experimental annotations. Reason: Core process for MCAD, redundantly supported. Propagation Review Root cause: NO FAILURE CORE Sources checked: ARBA:ARBA00085069 UNRESOLVED The proximate ARBA rule is identified, but its predicates and training evidence were not inspected. The annotation judgment uses independent human biochemical or localization evidence, not a claim that the rule internals were validated. UniProtKB:P45952 SUPPORTS TRANSFER Mouse Acadm donor identity is verified. The historical MGI comparative graph (2023-03-10) lists this term with IMP evidence from PMID:18459129; the exact current Ensembl transfer record was not re-extracted. Conserved MCAD chemistry and independent human enzyme assays support the target annotation. ensembl:ENSMUSP00000072483 SUPPORTS TRANSFER Mouse Acadm donor identity is verified. The historical MGI comparative graph (2023-03-10) lists this term with IMP evidence from PMID:18459129; the exact current Ensembl transfer record was not re-extracted. Conserved MCAD chemistry and independent human enzyme assays support the target annotation. Supporting Evidence: PMID:19224950 catalyzes the first step of the mitochondrial Ξ²-oxidation of medium-chain fatty acids |
| GO:0051791 medium-chain fatty acid metabolic process | IEA GO_REF:0000120 | ACCEPT | Summary: Automated annotation to medium-chain fatty acid metabolism. Accurate for MCAD; the catabolic child term (GO:0051793) is more precise but this parent is also correct and directly supported (PMID:1970566). Reason: MCAD acts on medium-chain fatty acids; this process term is correct. Propagation Review Root cause: NO FAILURE CORE Sources checked: ARBA:ARBA00089978 UNRESOLVED The proximate ARBA rule is identified, but its predicates and training evidence were not inspected. The annotation judgment uses independent human biochemical or localization evidence, not a claim that the rule internals were validated. UniProtKB:P45952 SUPPORTS TRANSFER Mouse Acadm donor identity is verified. The historical MGI comparative graph (2023-03-10) lists this term with IMP evidence from PMID:18459129; the exact current Ensembl transfer record was not re-extracted. Conserved MCAD chemistry and independent human enzyme assays support the target annotation. ensembl:ENSMUSP00000072483 SUPPORTS TRANSFER Mouse Acadm donor identity is verified. The historical MGI comparative graph (2023-03-10) lists this term with IMP evidence from PMID:18459129; the exact current Ensembl transfer record was not re-extracted. Conserved MCAD chemistry and independent human enzyme assays support the target annotation. Supporting Evidence: PMID:19224950 catalyzes the first step of the mitochondrial Ξ²-oxidation of medium-chain fatty acids |
| GO:0005739 mitochondrion | IDA GO_REF:0000052 | ACCEPT | Summary: HPA immunofluorescence evidence places ACADM in mitochondria, the organelle where its core catalytic activity occurs. Reason: The broad location accurately describes a core compartment. The more precise matrix annotation does not make mitochondrial residence a peripheral function. Independent human evidence corroborates the source; the individual imaging record was not re-extracted. Supporting Evidence: PMID:1902818 Demonstration of intra-mitochondrial mature MCAD indistinguishable in size (42.5-kDa) from control MCAD |
| GO:0070991 medium-chain fatty acyl-CoA dehydrogenase activity | EXP PMID:21237683 Identification and characterization of new long chain acyl-C... | ACCEPT | Summary: The human tissue study includes MCAD substrate profiles and neuronal distribution despite its focus on newly characterized ACAD10/11. Reason: Primary sections 3.7/3.8 and the Figure 6 discussion compare liver matrix activity with MCAD and SCAD profiles. The medium-chain assignment is independently established by purified human MCAD assays; the paper title naming other ACADs is not evidence of misattribution. Supporting Evidence: PMID:3597357 The products of SCA dehydrogenase/butyryl-CoA, MCA dehydrogenase/octanoyl-CoA, and IV dehydrogenase/isovaleryl-CoA reactions were identified as crotonyl-CoA, 2-octenoyl-CoA, and 3-methylcrotonyl-CoA |
| GO:0070991 medium-chain fatty acyl-CoA dehydrogenase activity | EXP PMID:8823175 Medium-long-chain chimeric human Acyl-CoA dehydrogenase: med... | ACCEPT | Summary: Direct experimental annotation from detailed kinetic/substrate-specificity characterization of recombinant human MCAD, establishing the medium-chain optimum (hexanoyl/octanoyl-CoA). Core molecular function. Reason: Experimentally supported core molecular function; the study defines MCAD's chain-length specificity and active-site base. Supporting Evidence: PMID:8823175 The catalytically essential glutamate residue that initiates catalysis by abstracting the substrate alpha-hydrogen as H+ is located at position 376 (mature MCADH numbering) on loop JK in medium chain acyl-CoA dehydrogenase (MCADH) |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | ACCEPT | Summary: The MitoCoP HTP annotation assigns ACADM to mitochondria, consistent with targeted studies. Reason: The full cached article describes the proteomic workflow, but its ACADM-specific supplementary identification was not independently re-extracted. Retain with curator deference and independent human mitochondrial localization evidence. A generic count of proteome proteins is not treated as gene-specific detection. Supporting Evidence: PMID:1902818 Demonstration of intra-mitochondrial mature MCAD indistinguishable in size (42.5-kDa) from control MCAD |
| GO:0005759 mitochondrial matrix | IDA PMID:16020546 Human acyl-CoA dehydrogenase-9 plays a novel role in the mit... | ACCEPT | Summary: The 2005 study directly assayed MCAD as a comparator in fractionated human muscle mitochondria. Reason: The primary full text and Figure 5 show MCAD in the matrix fraction as well as the membrane fraction; the authors describe MCAD as a matrix-localized ACAD. This supports the matrix location despite ACAD9 being the principal study subject. The full primary passage was inspected on the author-uploaded article; the local publication cache remains abstract-only. Supporting Evidence: file:human/ACADM/ACADM-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion matrix |
| GO:0031966 mitochondrial membrane | IDA PMID:16020546 Human acyl-CoA dehydrogenase-9 plays a novel role in the mit... | KEEP AS NON CORE | Summary: MCAD was directly detected in both matrix and membrane fractions in the 2005 human muscle experiment. Reason: Retain the observed membrane association as non-core. The full source interprets the membrane signal as loose association or nonspecific adherence typical of matrix ACADs; it does not establish an integral membrane protein or a distinct membrane-specific activity. The prior rationale wrongly dismissed the detection from MCAD being a matrix enzyme. Physiological membrane residence remains less secure than the matrix localization. |
| GO:0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase | IDA PMID:3597357 Purification and properties of short chain acyl-CoA, medium ... | ACCEPT | Summary: Direct annotation from purification and characterization of human liver MCAD, which identified the octanoyl-CoA dehydrogenation product (2-octenoyl-CoA) and ETF-dependent activity. Core process annotation. Reason: Purified human MCAD carries out the ETF-dependent acyl-CoA dehydrogenase step of beta-oxidation. Supporting Evidence: PMID:3597357 They all utilized electron transfer flavoprotein (ETF) or phenazine methosulfate (PMS) as an electron acceptor |
| GO:0070991 medium-chain fatty acyl-CoA dehydrogenase activity | IDA PMID:3597357 Purification and properties of short chain acyl-CoA, medium ... | ACCEPT | Summary: Direct annotation from purification of human liver MCAD, which converted octanoyl-CoA to 2-octenoyl-CoA and showed homotetrameric structure with 1 FAD per subunit. Core molecular function with classic biochemical support. Reason: Purified human MCAD has medium-chain acyl-CoA dehydrogenase activity; core MF. Supporting Evidence: PMID:3597357 The products of SCA dehydrogenase/butyryl-CoA, MCA dehydrogenase/octanoyl-CoA, and IV dehydrogenase/isovaleryl-CoA reactions were identified as crotonyl-CoA, 2-octenoyl-CoA, and 3-methylcrotonyl-CoA |
| GO:0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase | IDA PMID:25416781 Human METTL20 is a mitochondrial lysine methyltransferase th... | ACCEPT | Summary: Annotation supported by the METTL20/ETFbeta-KMT study, which assayed MCAD as a model ETF-dependent acyl-CoA dehydrogenase and showed ETFbeta methylation reduces electron transfer from MCAD. This confirms MCAD operates in the ETF-coupled beta-oxidation step. Reason: MCAD's role in ETF-coupled acyl-CoA dehydrogenase beta-oxidation is directly assayed here. Supporting Evidence: PMID:25416781 METTL20-mediated methylation of ETFΞ² in vitro reduced its ability to receive electrons from the medium chain acyl-CoA dehydrogenase and the glutaryl-CoA dehydrogenase |
| GO:0005634 nucleus | HDA PMID:21630459 Proteomic characterization of the human sperm nucleus. | UNDECIDED | Summary: ACADM has a nucleus HDA annotation from a purified human sperm-nucleus proteome, but the gene-specific identification could not be independently recovered. Reason: The abstract reports extensive removal of non-nuclear structures and high sample purity. Neither mitochondrial targeting nor the usual matrix activity disproves an additional sperm nuclear pool. Full text and the ACADM-specific supplementary record were not recovered from the publisher access attempt, so the prior contamination assertion is withdrawn and the annotation remains undecided. Supporting Evidence: PMID:21630459 sperm nuclei were obtained through CTAB treatment and isolated to over 99.9% purity without any tail fragments, acrosome or mitochondria |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-109341 | ACCEPT | Summary: The Reactome unsaturated medium-chain substrate reaction places ACADM in the mitochondrial matrix. Reason: The reaction context is compatible with MCAD chemistry and the matrix location is independently supported by human fractionation in PMID:16020546. The short cached pathway summary is not itself a localization experiment. Supporting Evidence: Reactome:R-HSA-109341 4-cis-decenoyl-CoA transits through the first step of the saturated beta-oxidation spiral to yield 2-trans-4-cis-decadienoyl-CoA. |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-1989745 | ACCEPT | Summary: The Reactome expression event carries the location of the produced ACADM protein. Reason: Accept the mature protein matrix location, independently established by human fractionation and the UniProt record. This event does not imply that transcription or cytosolic translation occurs in the matrix. Supporting Evidence: Reactome:R-HSA-1989745 The ACADM gene is transcribed to yield mRNA and the mRNA is translated to yield protein. |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-77338 | ACCEPT | Summary: Reactome describes the matrix dehydrogenation of octanoyl-CoA by ACADM. Reason: The compartment agrees with independent fractionation, and the reaction lies within the experimentally established medium-chain substrate range. Supporting Evidence: Reactome:R-HSA-77338 ACADM in the mitochondrial matrix dehydrogenates octanoyl-CoA to form trans-oct-2-enoyl-CoA. |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-77345 | ACCEPT | Summary: Reactome describes the matrix dehydrogenation of decanoyl-CoA by ACADM. Reason: The compartment agrees with independent fractionation, and the reaction lies within the experimentally established medium-chain substrate range. Supporting Evidence: Reactome:R-HSA-77345 ACADM in the mitochondrial matrix dehydrogenates decanoyl-CoA to form trans-dec-2-enoyl-CoA. |
| GO:0030424 axon | IDA PMID:21237683 Identification and characterization of new long chain acyl-C... | KEEP AS NON CORE | Summary: Primary immunostaining detects MCAD in axons of selected human cerebellar neurons. Reason: Retain the observed neuronal compartment as non-core. This is compatible with mitochondrial localization, but the immunohistochemical observation alone does not resolve every stained molecule to mitochondria or establish an additional axon-specific molecular activity. Supporting Evidence: PMID:21237683 MCAD in the molecular layer and axons of specific neurons |
| GO:0005739 mitochondrion | IDA GO_REF:0000054 | ACCEPT | Summary: LIFEdb fusion-protein evidence places ACADM in mitochondria, the organelle where its core catalytic activity occurs. Reason: The broad location accurately describes a core compartment. The more precise matrix annotation does not make mitochondrial residence a peripheral function. Independent human evidence corroborates the source; the individual imaging record was not re-extracted. Supporting Evidence: PMID:1902818 Demonstration of intra-mitochondrial mature MCAD indistinguishable in size (42.5-kDa) from control MCAD |
| GO:0051791 medium-chain fatty acid metabolic process | IDA PMID:1970566 Characterization of wild-type and an active site mutant of h... | ACCEPT | Summary: Direct annotation from characterization of wild-type and active-site-mutant human MCAD expressed in E. coli, which established medium-chain acyl-CoA dehydrogenase function and the catalytic base. Core process annotation. Reason: MCAD acts on medium-chain fatty acids; directly supported by enzyme characterization. Supporting Evidence: PMID:1970566 Glu376 plays an important role in the initial step of dehydrogenation catalysis |
| GO:0051793 medium-chain fatty acid catabolic process | IDA PMID:1970566 Characterization of wild-type and an active site mutant of h... | ACCEPT | Summary: Direct annotation of MCAD's role in medium-chain fatty acid catabolism, from the same enzyme-characterization study. Core catabolic process annotation. Reason: MCAD catabolizes medium-chain fatty acids; directly supported. Supporting Evidence: PMID:1970566 Glu376 plays an important role in the initial step of dehydrogenation catalysis |
| GO:0070991 medium-chain fatty acyl-CoA dehydrogenase activity | IDA PMID:19224950 Protein misfolding is the molecular mechanism underlying MCA... | ACCEPT | Summary: Direct annotation from biochemical characterization of recombinant human MCAD and disease variants, including octanoyl-CoA kinetics (WT KM 0.4 uM octanoyl-CoA). Core molecular function with strong support. Reason: Purified human MCAD has medium-chain (octanoyl-CoA) dehydrogenase activity; core MF. Supporting Evidence: PMID:19224950 Maximum activities (Vmax) and apparent substrate affinities (Km) of octanoyl-CoA oxidation were determined by MichaelisβMenten kinetics |
| GO:0070991 medium-chain fatty acyl-CoA dehydrogenase activity | IDA PMID:1970566 Characterization of wild-type and an active site mutant of h... | ACCEPT | Summary: Direct annotation from the wild-type/active-site-mutant MCAD study; the WT enzyme had specific activity 50% of MCAD purified from pig kidney and contained stoichiometric FAD, while the catalytic-base mutant was inactive. Core molecular function. Reason: Directly demonstrated medium-chain acyl-CoA dehydrogenase activity dependent on the active-site glutamate and FAD. Supporting Evidence: PMID:1970566 The wild-type enzyme is a yellow protein due to the content of stoichiometric FAD and had a specific activity which is 50% of MCADH purified from pig kidney |
| GO:0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase | IDA PMID:1902818 Molecular characterization of medium-chain acyl-CoA dehydrog... | ACCEPT | Summary: The recombinant human disease variant was inactive and was proposed to have impaired tetramer formation. Reason: The source supports loss of the known MCAD catalytic activity; tetramer failure is presented as a probable explanation in its abstract, not a directly resolved mechanism for every variant. Independent purified human MCAD data establish the ETF-dependent beta-oxidation step. Supporting Evidence: PMID:1902818 mutant MCAD, which was demonstrated to be inactive, probably because of the inability to form active tetrameric MCAD PMID:3597357 The products of SCA dehydrogenase/butyryl-CoA, MCA dehydrogenase/octanoyl-CoA, and IV dehydrogenase/isovaleryl-CoA reactions were identified as crotonyl-CoA, 2-octenoyl-CoA, and 3-methylcrotonyl-CoA |
| GO:0070991 medium-chain fatty acyl-CoA dehydrogenase activity | IDA PMID:1902818 Molecular characterization of medium-chain acyl-CoA dehydrog... | ACCEPT | Summary: Direct annotation of MCAD medium-chain dehydrogenase activity from the MCAD-deficiency characterization, in which expression of the K329E mutant produced inactive enzyme. Core molecular function (loss-of-function demonstrates the activity). Reason: The disease mutant abolishes MCAD activity, supporting the medium-chain dehydrogenase MF. Supporting Evidence: PMID:1902818 mutant MCAD, which was demonstrated to be inactive, probably because of the inability to form active tetrameric MCAD |
| GO:0019254 carnitine metabolic process, CoA-linked | IMP PMID:16972171 Prolonged moderate-intensity exercise without and with L-car... | UNDECIDED | Summary: The exercise study links MCAD deficiency to changes in carnitine pools and inferred compensatory biosynthesis. Reason: The accessible abstract measures patient plasma/urine metabolites and interprets increased free carnitine and gamma-butyrobetaine as compensation for carnitine loss. That does not by itself demonstrate that ACADM performs a step in carnitine metabolic process, CoA-linked. The full paper was not recovered, so a stronger judgment about the experimental annotation is deferred. The prior non-core acceptance is not retained merely because the annotation uses IMP. Supporting Evidence: PMID:16972171 Our results suggest that MCADD patients are able to increase carnitine biosynthesis during exercise to compensate for carnitine losses |
| GO:0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase | IMP PMID:16972171 Prolonged moderate-intensity exercise without and with L-car... | ACCEPT | Summary: The patient exercise study is consistent with MCAD-dependent medium-chain fatty acid oxidation in vivo. Reason: The rise in free fatty acids and octanoylcarnitine reports substrate mobilization and accumulation during exercise, rather than directly quantifying successful flux through the blocked MCAD reaction. Retain the known beta-oxidation involvement using independent purified-enzyme evidence and curator deference. Supporting Evidence: PMID:16972171 A significant rise in plasma free fatty acids and octanoylcarnitine levels during exercise was seen in all patients PMID:3597357 The products of SCA dehydrogenase/butyryl-CoA, MCA dehydrogenase/octanoyl-CoA, and IV dehydrogenase/isovaleryl-CoA reactions were identified as crotonyl-CoA, 2-octenoyl-CoA, and 3-methylcrotonyl-CoA |
| GO:0045329 carnitine biosynthetic process | IMP PMID:16972171 Prolonged moderate-intensity exercise without and with L-car... | UNDECIDED | Summary: The exercise study links MCAD deficiency to changes in carnitine pools and inferred compensatory biosynthesis. Reason: The accessible abstract measures patient plasma/urine metabolites and interprets increased free carnitine and gamma-butyrobetaine as compensation for carnitine loss. That does not by itself demonstrate that ACADM performs a step in carnitine biosynthetic process. The full paper was not recovered, so a stronger judgment about the experimental annotation is deferred. The prior non-core acceptance is not retained merely because the annotation uses IMP. Supporting Evidence: PMID:16972171 Our results suggest that MCADD patients are able to increase carnitine biosynthesis during exercise to compensate for carnitine losses |
| GO:0003995 acyl-CoA dehydrogenase activity | IDA PMID:19224950 Protein misfolding is the molecular mechanism underlying MCA... | ACCEPT | Summary: ACADM has acyl-CoA dehydrogenase activity, as demonstrated by its FAD-dependent acyl-CoA dehydrogenation. Reason: This broader catalytic class correctly describes the same core reaction as the medium-chain child term. Breadth alone does not make a core enzyme activity non-core. Supporting Evidence: PMID:19224950 Maximum activities (Vmax) and apparent substrate affinities (Km) of octanoyl-CoA oxidation were determined by MichaelisβMenten kinetics |
| GO:0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase | IDA PMID:19224950 Protein misfolding is the molecular mechanism underlying MCA... | ACCEPT | Summary: Direct annotation from MCAD variant characterization establishing the enzyme's role in the acyl-CoA dehydrogenase step of beta-oxidation, with loss-of-function variants causing MCADD. Core process. Reason: MCAD carries out the acyl-CoA dehydrogenase step of beta-oxidation; loss causes disease. Supporting Evidence: PMID:19224950 MCAD is a member of the acyl-CoA dehydrogenase (ACAD) family of flavoproteins, which catalyzes the first step of the mitochondrial Ξ²-oxidation of medium-chain fatty acids |
| GO:0042802 identical protein binding | IDA PMID:19224950 Protein misfolding is the molecular mechanism underlying MCA... | KEEP AS NON CORE | Summary: Purified wild-type human MCAD forms a homotetramer, providing direct evidence for identical-protein association. Reason: Retain the self-association property while describing the enzyme chemistry as its core function. Size-exclusion data and disease-variant assembly defects in PMID:19224950 substantiate the association. No specific adaptor activity or new oligomerization process is inferred from binding alone. Supporting Evidence: PMID:19224950 Wild-type MCAD was eluted in the tetrameric form with an almost negligible amount of aggregates |
| GO:0005739 mitochondrion | TAS PMID:1731887 Structural organization and regulatory regions of the human ... | ACCEPT | Summary: The human gene-structure paper explicitly describes MCAD as a mitochondrial flavoenzyme. Reason: Retain the organelle location as core, corroborated by protein-level localization and later fractionation; the source is a traceable statement rather than a new localization assay. Supporting Evidence: PMID:1731887 Medium-chain acyl-CoA dehydrogenase (MCAD) is a highly regulated mitochondrial flavo-enzyme that catalyzes the initial reaction in fatty acid beta-oxidation |
| GO:0003995 acyl-CoA dehydrogenase activity | IMP PMID:2393404 Identification of a common mutation in patients with medium-... | ACCEPT | Summary: ACADM has acyl-CoA dehydrogenase activity, as demonstrated by its FAD-dependent acyl-CoA dehydrogenation. Reason: The source identifies a disease-associated ACADM variant; it is not itself a purified-enzyme substrate panel. The inferred enzyme activity is independently established by human biochemical studies, so retain the broad core activity with curator deference. Supporting Evidence: PMID:2393404 A single A to G nucleotide replacement which resulted in lysine329-to-glutamic acid329 substitution of the MCAD protein was identified in all cultures PMID:3597357 The products of SCA dehydrogenase/butyryl-CoA, MCA dehydrogenase/octanoyl-CoA, and IV dehydrogenase/isovaleryl-CoA reactions were identified as crotonyl-CoA, 2-octenoyl-CoA, and 3-methylcrotonyl-CoA |
| GO:0006635 fatty acid beta-oxidation | IMP PMID:2393404 Identification of a common mutation in patients with medium-... | ACCEPT | Summary: The source identifies a common ACADM mutation in MCAD-deficient patient fibroblasts. Reason: Retain the core beta-oxidation process with curator deference and independent human biochemical evidence. The genetic association abstract does not independently quantify pathway flux or resolve the variant folding mechanism. Supporting Evidence: PMID:2393404 A single A to G nucleotide replacement which resulted in lysine329-to-glutamic acid329 substitution of the MCAD protein was identified in all cultures PMID:3597357 The products of SCA dehydrogenase/butyryl-CoA, MCA dehydrogenase/octanoyl-CoA, and IV dehydrogenase/isovaleryl-CoA reactions were identified as crotonyl-CoA, 2-octenoyl-CoA, and 3-methylcrotonyl-CoA |
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Download this section (compressed HTML)Q: What experiments resolve genuine ACADM residence in sperm nuclei, beyond identification in a purified nuclear proteome?
Q: What mechanism connects MCAD-dependent fatty-acid oxidation to the CoA-linked carnitine process beyond altered acylcarnitine pools, and how do the mouse stress-dependent glucose-flux findings translate to human tissues?
Q: What proportion of human MCAD activity on short- and long-chain substrates contributes to physiological flux in different tissues, compared with its dominant medium-chain role?
Experiment: Quantitative substrate-profiling of purified recombinant human MCAD across C4-C16 saturated and unsaturated acyl-CoAs using the ETF-coupled assay, to define the precise chain-length boundaries and rank-order efficiency that justify the medium-chain vs long-chain MF annotations and to test whether the C14/C16 RHEA-derived long-chain annotations are physiologically meaningful.
Experiment: Use orthogonal localization assays and ACADM-specific peptide validation in purified human sperm nuclei to distinguish a genuine nuclear pool from preparation artifacts. In parallel, assess the reproducibility and physiological context of MCAD membrane association with controlled mitochondrial fractionation.
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