MCEE encodes methylmalonyl-CoA epimerase (also called DL-methylmalonyl-CoA racemase; EC 5.1.99.1), a mitochondrial matrix enzyme of the vicinal-oxygen-chelate (VOC)/glyoxalase superfamily. It catalyses the interconversion of (2R)- and (2S)-methylmalonyl-CoA (D- and L-methylmalonyl-CoA), the epimerisation step that lies between propionyl-CoA carboxylase (PCC) and methylmalonyl-CoA mutase (MMUT) in the propionyl-CoA catabolic pathway. Propionyl-CoA arising from catabolism of the branched-chain and other amino acids (valine, isoleucine, threonine, methionine), odd-chain fatty acids, and cholesterol is carboxylated by PCC to (2S)-methylmalonyl-CoA, epimerised by MCEE to the (2R)/(S)-isomer that MMUT requires, and rearranged by MMUT to succinyl-CoA for entry into the citric acid cycle. The mature enzyme (after cleavage of an N-terminal mitochondrial transit peptide) binds a divalent metal ion, with cobalt modelled at the active site in the crystal structure. Loss-of-function variants cause methylmalonyl-CoA epimerase deficiency (MCEED), a usually mild autosomal recessive methylmalonic aciduria.
Definition: Binding of a metal ion (a divalent cation, with cobalt modelled in the MCEE crystal structure) by methylmalonyl-CoA epimerase at its vicinal-oxygen-chelate active site.
Justification: UniProt annotates MCEE with the keywords Cobalt and Metal-binding and the crystal structure (PDB 3RMU/6QH4) models a divalent metal (Co2+) coordinated by residues His50/Gln122/Glu172 in the VOC active site. The GO:0046872 metal ion binding IEA annotation is present in the UniProt cross-reference block but not in the current GOA TSV; it is biologically well supported and could be added (GO:0046872 already exists).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004493 methylmalonyl-CoA epimerase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) assignment of the defining molecular function of MCEE. Fully consistent with the experimental characterisation of the human enzyme. Reason: This is the core molecular function of MCEE and is directly supported by the experimental IDA annotation from PMID:11481338 as well as the EC/RHEA mapping. Supporting Evidence: PMID:11481338 Subsequent biochemical studies confirmed this inference by showing that the prokaryotic gene PH0272 and its human homologue both encode DL-methylmalonyl-CoA racemases. |
| GO:0046491 L-methylmalonyl-CoA metabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) assignment of involvement in L-methylmalonyl-CoA metabolism, the process directly defined by the enzyme's substrate/product. Reason: MCEE interconverts D- and L-methylmalonyl-CoA, so it is directly involved in L-methylmalonyl-CoA metabolism. Duplicated by the experimental IDA line (PMID:11481338); both are correct. Supporting Evidence: Reactome:R-HSA-71020 This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'methylmalonyl-CoA epimerase activity' of 'methylmalonyl-CoA epimerase'. |
| GO:0004493 methylmalonyl-CoA epimerase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic mapping of EC 5.1.99.1 / RHEA:20553 to the epimerase molecular function. Reason: Correct EC/Rhea-based mapping of the enzyme's activity; the underlying EC assignment is experimentally validated (PMID:11481338). Redundant with the IBA/IDA/TAS lines for the same term but the mapping itself is sound. Supporting Evidence: PMID:11481338 Subsequent biochemical studies confirmed this inference by showing that the prokaryotic gene PH0272 and its human homologue both encode DL-methylmalonyl-CoA racemases. |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic SubCell mapping (SL-0173 Mitochondrion) of MCEE localisation. Reason: MCEE has an N-terminal mitochondrial transit peptide (residues 1-36) and a UniProt SUBCELLULAR LOCATION of Mitochondrion; localisation is corroborated by experimental mito-proteome data (PMID:34800366) and Reactome (matrix). The more specific mitochondrial matrix term is captured elsewhere. Supporting Evidence: Reactome:R-HSA-71020 This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'methylmalonyl-CoA epimerase activity' of 'methylmalonyl-CoA epimerase'. |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | MARK AS OVER ANNOTATED | Summary: Bare "protein binding" from a systematic proteome-scale binary (Y2H) interactome map. Reason: "Protein binding" (GO:0005515) is uninformative and is derived here from a high-throughput binary interactome screen rather than a targeted study of MCEE. The reported interactors (AGTRAP, CMTM5 in this record; CD81, STX8 elsewhere) are membrane/trafficking proteins with no plausible functional relationship to a soluble mitochondrial-matrix epimerase, consistent with systematic-screen artifacts. Retained but flagged as over-annotation per curation policy (experimental IPI, so not removed). Supporting Evidence: PMID:25416956 screening half of the interactome space with minimal |
| GO:0005515 protein binding | IPI PMID:25910212 Widespread macromolecular interaction perturbations in human... | MARK AS OVER ANNOTATED | Summary: Bare "protein binding" from a large-scale interactome-perturbation study. Reason: Uninformative "protein binding" from a high-throughput interactome dataset; the AGTRAP/CMTM5 interactions carry no functional insight for MCEE's epimerase activity. Flagged as over-annotation (experimental IPI, not removed). Supporting Evidence: PMID:25910212 Widespread macromolecular interaction perturbations in human genetic disorders |
| GO:0005515 protein binding | IPI PMID:31515488 Extensive disruption of protein interactions by genetic vari... | MARK AS OVER ANNOTATED | Summary: Bare "protein binding" from a large-scale variant/protein-interaction screen. Reason: Uninformative "protein binding" from a high-throughput PPI screen (AGTRAP, CMTM5); no bearing on MCEE's known molecular function. Flagged as over-annotation (experimental IPI, not removed). Supporting Evidence: PMID:31515488 disruption of protein interactions by genetic variants |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Bare "protein binding" from the HuRI reference binary interactome. Reason: Uninformative "protein binding" from the systematic HuRI binary interactome; the reported partners (CD81, AGTRAP, CMTM5, STX8 across records) are surface/trafficking proteins unrelated to a matrix epimerase. Flagged as over-annotation (experimental IPI, not removed). Supporting Evidence: PMID:32296183 reference map of the human binary protein interactome |
| GO:0019626 short-chain fatty acid catabolic process | TAS Reactome:R-HSA-71032 | ACCEPT | Summary: Author-asserted (Reactome) involvement in propionyl-CoA catabolism, annotated to the short-chain fatty acid catabolic process parent. Reason: MCEE catalyses one of the three reactions of the propionyl-CoA catabolic pathway, which converts propionyl-CoA (a short-chain acyl-CoA derived from odd-chain fatty acids and amino-acid catabolism) to succinyl-CoA. The annotation correctly places MCEE in this catabolic process, though it is broader than the more specific methylmalonyl-CoA terms. Supporting Evidence: Reactome:R-HSA-71032 The three reactions of this pathway convert propionyl-CoA to succinyl-CoA, an intermediate of the citric acid cycle. |
| GO:0004493 methylmalonyl-CoA epimerase activity | TAS Reactome:R-HSA-71020 | ACCEPT | Summary: Author-asserted (Reactome) epimerase molecular function. Reason: Reactome traceably assigns the methylmalonyl-CoA epimerase activity to MCEE for the D-/L-methylmalonyl-CoA interconversion reaction; concordant with the experimental IDA. Core molecular function (duplicate of the IBA/IEA/IDA lines). Supporting Evidence: Reactome:R-HSA-71020 This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'methylmalonyl-CoA epimerase activity' of 'methylmalonyl-CoA epimerase'. |
| GO:0005739 mitochondrion | TAS PMID:11481338 Identification of the human methylmalonyl-CoA racemase gene ... | ACCEPT | Summary: Traceable assertion that MCEE is active in the mitochondrion. Reason: Consistent with the mitochondrial transit peptide, UniProt SUBCELLULAR LOCATION, and the enzyme's role in the mitochondrial propionyl-CoA pathway. The mitochondrial matrix (GO:0005759) term is more specific. Supporting Evidence: PMID:11481338 human DL-methylmalonyl-CoA racemase gene |
| GO:1901290 succinyl-CoA biosynthetic process | IDA PMID:11481338 Identification of the human methylmalonyl-CoA racemase gene ... | ACCEPT | Summary: Experimental (IDA) involvement in succinyl-CoA biosynthesis, the end product of the propionyl-CoA catabolic pathway in which MCEE acts. Reason: MCEE is the epimerase step immediately upstream of methylmalonyl-CoA mutase, which produces succinyl-CoA; MCEE is therefore genuinely involved in succinyl-CoA biosynthesis. Curator-attributed experimental annotation from the defining paper; retained (the process describes the pathway outcome rather than MCEE's direct chemistry, which is captured by the methylmalonyl-CoA terms). Supporting Evidence: PMID:11481338 both encode DL-methylmalonyl-CoA racemases Reactome:R-HSA-71032 The three reactions of this pathway convert propionyl-CoA to succinyl-CoA, an intermediate of the citric acid cycle. |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | ACCEPT | Summary: High-throughput mitochondrial-proteome detection of MCEE. Reason: MCEE is present in the high-confidence human mitochondrial proteome, corroborating the mitochondrial localisation from sequence-based prediction and Reactome. The matrix term (GO:0005759) is the most specific location. Supporting Evidence: PMID:34800366 Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context. |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-71020 | ACCEPT | Summary: Author-asserted (Reactome) localisation to the mitochondrial matrix. Reason: The propionyl-CoA catabolic reactions, including the MCEE epimerase step, take place in the mitochondrial matrix. This is the most specific and appropriate location term for MCEE. Supporting Evidence: Reactome:R-HSA-71020 This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'methylmalonyl-CoA epimerase activity' of 'methylmalonyl-CoA epimerase'. |
| GO:0004493 methylmalonyl-CoA epimerase activity | IDA PMID:11481338 Identification of the human methylmalonyl-CoA racemase gene ... | ACCEPT | Summary: Direct experimental demonstration that the human MCEE gene product is a DL-methylmalonyl-CoA racemase (epimerase). Reason: This is the primary experimental evidence for MCEE's core molecular function (EC 5.1.99.1); Bobik & Rasche biochemically confirmed racemase activity for the human homolog. Definitive core-function annotation. Supporting Evidence: PMID:11481338 Subsequent biochemical studies confirmed this inference by showing that the prokaryotic gene PH0272 and its human homologue both encode DL-methylmalonyl-CoA racemases. |
| GO:0046491 L-methylmalonyl-CoA metabolic process | IDA PMID:11481338 Identification of the human methylmalonyl-CoA racemase gene ... | ACCEPT | Summary: Experimental (IDA) involvement in L-methylmalonyl-CoA metabolism. Reason: MCEE's characterised epimerase activity directly interconverts D- and L-methylmalonyl-CoA, so it is directly involved in L-methylmalonyl-CoA metabolism. Core biological process; duplicates the IBA line for the same term. Supporting Evidence: PMID:11481338 both encode DL-methylmalonyl-CoA racemases |
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Download this section (compressed HTML)Q: What is the physiologically relevant catalytic metal ion for human MCEE in vivo (cobalt was used in the crystallization, but the native cofactor may differ)?
Q: Do the reported binary interactors (AGTRAP, CD81, CMTM5, STX8) reflect any genuine physiological association, or are they artifacts of high-throughput Y2H screens given MCEE's mitochondrial-matrix localisation?
Experiment: Determine the metal-ion specificity and catalytic parameters of recombinant human MCEE with different divalent cations (Co2+, Mg2+, Mn2+, Zn2+) to establish the native cofactor.
Experiment: Assess flux through the propionyl-CoA pathway and metabolite accumulation (methylmalonic acid, propionylcarnitine) in MCEE-knockout versus wild-type cells to quantify the contribution of the epimerase step relative to non-enzymatic epimerisation.
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