id: Q96PE7
gene_symbol: MCEE
product_type: PROTEIN
status: INITIALIZED
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  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.
references:
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      PAN-GO/GO_Central phylogenetic (IBA) inference for the MCEE ortholog group; consistent
      with the well-established epimerase function and mitochondrial localisation.
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      SubCell mapping (SL-0173 Mitochondrion) to GO:0005739; consistent with the UniProt
      SUBCELLULAR LOCATION and experimental mitochondrial-proteome data.
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      EC 5.1.99.1 / RHEA:20553 to GO:0004493 mapping; the EC and Rhea assignments are
      experimentally supported (PMID:11481338) so this electronic mapping is correct.
- id: PMID:11481338
  title: Identification of the human methylmalonyl-CoA racemase gene based on the
    analysis of prokaryotic gene arrangements. Implications for decoding the human
    genome.
  findings:
  - statement: >-
      Identified the human DL-methylmalonyl-CoA racemase (MCEE) gene and confirmed
      biochemically that the human protein and its prokaryotic homolog both encode
      DL-methylmalonyl-CoA racemases (epimerases) acting in propionyl-CoA metabolism.
    supporting_text: >-
      Subsequent biochemical studies confirmed this inference by showing that the
      prokaryotic gene PH0272 and its human homologue both encode DL-methylmalonyl-CoA
      racemases.
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Primary paper establishing MCEE function and catalytic activity; PubMed-verified.
      Basis for the experimental (IDA) GO:0004493, GO:0046491 and GO:1901290 annotations.
- id: PMID:25416956
  title: A proteome-scale map of the human interactome network.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Systematic proteome-scale binary (Y2H) interactome map (HI-II-14). Source of a
      high-throughput "protein binding" IPI; no MCEE-specific functional insight.
- id: PMID:25910212
  title: Widespread macromolecular interaction perturbations in human genetic disorders.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Large-scale interactome-perturbation study; source of a high-throughput "protein
      binding" IPI, uninformative for MCEE molecular function.
- id: PMID:31515488
  title: Extensive disruption of protein interactions by genetic variants across the
    allele frequency spectrum in human populations.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Large-scale variant/PPI screen; source of a high-throughput "protein binding" IPI,
      not a targeted study of MCEE.
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      HuRI reference binary interactome (Y2H); source of a high-throughput "protein
      binding" IPI, uninformative for MCEE function.
- id: PMID:34800366
  title: Quantitative high-confidence human mitochondrial proteome and its dynamics
    in cellular context.
  findings:
  - statement: >-
      MCEE is detected in the high-confidence human mitochondrial proteome, supporting
      its mitochondrial localisation.
    supporting_text: >-
      Quantitative high-confidence human mitochondrial proteome and its dynamics in
      cellular context.
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      High-throughput (HTP) mitochondrial-proteome study; corroborates the mitochondrion
      localisation. Supporting_text is the study title (full text >256KB, not inspected line-by-line).
- id: PMID:16752391
  title: A homozygous nonsense mutation in the methylmalonyl-CoA epimerase gene (MCEE)
    results in mild methylmalonic aciduria.
  full_text_unavailable: true
  findings:
  - statement: >-
      A homozygous nonsense mutation in MCEE causes methylmalonyl-CoA epimerase deficiency
      (MCEED), a mild methylmalonic aciduria, confirming a physiological role for MCEE in
      propionyl-CoA/methylmalonyl-CoA catabolism.
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Establishes MCEE deficiency as a human disease (MIM:251120); referenced in UniProt
      (INVOLVEMENT IN MCEED). Not cited as an existing GOA annotation but relevant to
      MCEE's biological role. Cached publication not available (abstract-only); title
      matches the UniProt cross-reference.
- id: Reactome:R-HSA-71020
  title: D-methylmalonyl-CoA <=> L-methylmalonyl-CoA
  findings:
  - statement: >-
      MCEE mediates the reversible interconversion of D- and L-methylmalonyl-CoA in the
      mitochondrial matrix.
    supporting_text: >-
      This reaction takes place in the 'mitochondrial matrix' and  is mediated by the
      'methylmalonyl-CoA epimerase activity' of 'methylmalonyl-CoA epimerase'.
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Reactome reaction for the epimerase step; consistent with UniProt catalytic activity
      and mitochondrial-matrix localisation.
- id: Reactome:R-HSA-71032
  title: Propionyl-CoA catabolism
  findings:
  - statement: >-
      The three-reaction propionyl-CoA catabolic pathway (including the MCEE epimerase step)
      converts propionyl-CoA to succinyl-CoA in the mitochondrial matrix.
    supporting_text: >-
      The three reactions of this pathway convert propionyl-CoA to succinyl-CoA, an
      intermediate of the citric acid cycle.
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Reactome pathway placing MCEE in propionyl-CoA catabolism; supports the
      short-chain fatty acid catabolic process annotation.
existing_annotations:
- term:
    id: GO:0004493
    label: methylmalonyl-CoA epimerase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      Phylogenetic (IBA) assignment of the defining molecular function of MCEE. Fully
      consistent with the experimental characterisation of the human enzyme.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:11481338
      supporting_text: >-
        Subsequent biochemical studies confirmed this inference by showing that the
        prokaryotic gene PH0272 and its human homologue both encode DL-methylmalonyl-CoA
        racemases.
- term:
    id: GO:0046491
    label: L-methylmalonyl-CoA metabolic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Phylogenetic (IBA) assignment of involvement in L-methylmalonyl-CoA metabolism, the
      process directly defined by the enzyme's substrate/product.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: Reactome:R-HSA-71020
      supporting_text: >-
        This reaction takes place in the 'mitochondrial matrix' and  is mediated by the
        'methylmalonyl-CoA epimerase activity' of 'methylmalonyl-CoA epimerase'.
- term:
    id: GO:0004493
    label: methylmalonyl-CoA epimerase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      Electronic mapping of EC 5.1.99.1 / RHEA:20553 to the epimerase molecular function.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:11481338
      supporting_text: >-
        Subsequent biochemical studies confirmed this inference by showing that the
        prokaryotic gene PH0272 and its human homologue both encode DL-methylmalonyl-CoA
        racemases.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: >-
      Electronic SubCell mapping (SL-0173 Mitochondrion) of MCEE localisation.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: Reactome:R-HSA-71020
      supporting_text: >-
        This reaction takes place in the 'mitochondrial matrix' and  is mediated by the
        'methylmalonyl-CoA epimerase activity' of 'methylmalonyl-CoA epimerase'.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25416956
  qualifier: enables
  review:
    summary: >-
      Bare "protein binding" from a systematic proteome-scale binary (Y2H) interactome map.
    action: MARK_AS_OVER_ANNOTATED
    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).
    supported_by:
    - reference_id: PMID:25416956
      supporting_text: >-
        screening half of the interactome space with minimal
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25910212
  qualifier: enables
  review:
    summary: >-
      Bare "protein binding" from a large-scale interactome-perturbation study.
    action: MARK_AS_OVER_ANNOTATED
    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).
    supported_by:
    - reference_id: PMID:25910212
      supporting_text: >-
        Widespread macromolecular interaction perturbations in human genetic disorders
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:31515488
  qualifier: enables
  review:
    summary: >-
      Bare "protein binding" from a large-scale variant/protein-interaction screen.
    action: MARK_AS_OVER_ANNOTATED
    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).
    supported_by:
    - reference_id: PMID:31515488
      supporting_text: >-
        disruption of protein interactions by genetic variants
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  qualifier: enables
  review:
    summary: >-
      Bare "protein binding" from the HuRI reference binary interactome.
    action: MARK_AS_OVER_ANNOTATED
    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).
    supported_by:
    - reference_id: PMID:32296183
      supporting_text: >-
        reference map of the human binary protein interactome
- term:
    id: GO:0019626
    label: short-chain fatty acid catabolic process
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-71032
  qualifier: involved_in
  review:
    summary: >-
      Author-asserted (Reactome) involvement in propionyl-CoA catabolism, annotated to the
      short-chain fatty acid catabolic process parent.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: Reactome:R-HSA-71032
      supporting_text: >-
        The three reactions of this pathway convert propionyl-CoA to succinyl-CoA, an
        intermediate of the citric acid cycle.
- term:
    id: GO:0004493
    label: methylmalonyl-CoA epimerase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-71020
  qualifier: enables
  review:
    summary: >-
      Author-asserted (Reactome) epimerase molecular function.
    action: ACCEPT
    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).
    supported_by:
    - reference_id: Reactome:R-HSA-71020
      supporting_text: >-
        This reaction takes place in the 'mitochondrial matrix' and  is mediated by the
        'methylmalonyl-CoA epimerase activity' of 'methylmalonyl-CoA epimerase'.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: TAS
  original_reference_id: PMID:11481338
  qualifier: is_active_in
  review:
    summary: >-
      Traceable assertion that MCEE is active in the mitochondrion.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:11481338
      supporting_text: >-
        human DL-methylmalonyl-CoA racemase gene
- term:
    id: GO:1901290
    label: succinyl-CoA biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:11481338
  qualifier: involved_in
  review:
    summary: >-
      Experimental (IDA) involvement in succinyl-CoA biosynthesis, the end product of the
      propionyl-CoA catabolic pathway in which MCEE acts.
    action: ACCEPT
    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).
    supported_by:
    - reference_id: PMID:11481338
      supporting_text: >-
        both encode DL-methylmalonyl-CoA racemases
    - reference_id: Reactome:R-HSA-71032
      supporting_text: >-
        The three reactions of this pathway convert propionyl-CoA to succinyl-CoA, an
        intermediate of the citric acid cycle.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HTP
  original_reference_id: PMID:34800366
  qualifier: located_in
  review:
    summary: >-
      High-throughput mitochondrial-proteome detection of MCEE.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:34800366
      supporting_text: >-
        Quantitative high-confidence human mitochondrial proteome and its dynamics in
        cellular context.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-71020
  qualifier: located_in
  review:
    summary: >-
      Author-asserted (Reactome) localisation to the mitochondrial matrix.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: Reactome:R-HSA-71020
      supporting_text: >-
        This reaction takes place in the 'mitochondrial matrix' and  is mediated by the
        'methylmalonyl-CoA epimerase activity' of 'methylmalonyl-CoA epimerase'.
- term:
    id: GO:0004493
    label: methylmalonyl-CoA epimerase activity
  evidence_type: IDA
  original_reference_id: PMID:11481338
  qualifier: enables
  review:
    summary: >-
      Direct experimental demonstration that the human MCEE gene product is a
      DL-methylmalonyl-CoA racemase (epimerase).
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:11481338
      supporting_text: >-
        Subsequent biochemical studies confirmed this inference by showing that the
        prokaryotic gene PH0272 and its human homologue both encode DL-methylmalonyl-CoA
        racemases.
- term:
    id: GO:0046491
    label: L-methylmalonyl-CoA metabolic process
  evidence_type: IDA
  original_reference_id: PMID:11481338
  qualifier: involved_in
  review:
    summary: >-
      Experimental (IDA) involvement in L-methylmalonyl-CoA metabolism.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:11481338
      supporting_text: >-
        both encode DL-methylmalonyl-CoA racemases
core_functions:
- description: >-
    Methylmalonyl-CoA epimerase (racemase) activity: reversible interconversion of
    (2R)- and (2S)-methylmalonyl-CoA (D-/L-methylmalonyl-CoA), the epimerisation step
    that provides methylmalonyl-CoA mutase (MMUT) with the isomer it requires.
  molecular_function:
    id: GO:0004493
    label: methylmalonyl-CoA epimerase activity
  directly_involved_in:
  - id: GO:0046491
    label: L-methylmalonyl-CoA metabolic process
  supported_by:
  - reference_id: PMID:11481338
    supporting_text: >-
      Subsequent biochemical studies confirmed this inference by showing that the
      prokaryotic gene PH0272 and its human homologue both encode DL-methylmalonyl-CoA
      racemases.
- description: >-
    In the mitochondrial matrix, MCEE performs the epimerase step of propionyl-CoA
    catabolism, feeding the mutase reaction that produces succinyl-CoA for the citric
    acid cycle.
  molecular_function:
    id: GO:0004493
    label: methylmalonyl-CoA epimerase activity
  directly_involved_in:
  - id: GO:0019626
    label: short-chain fatty acid catabolic process
  locations:
  - id: GO:0005759
    label: mitochondrial matrix
  supported_by:
  - reference_id: Reactome:R-HSA-71032
    supporting_text: >-
      The three reactions of this pathway convert propionyl-CoA to succinyl-CoA, an
      intermediate of the citric acid cycle.
  - reference_id: Reactome:R-HSA-71020
    supporting_text: >-
      This reaction takes place in the 'mitochondrial matrix' and  is mediated by the
      'methylmalonyl-CoA epimerase activity' of 'methylmalonyl-CoA epimerase'.
proposed_new_terms:
- proposed_name: metal ion binding
  proposed_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).
suggested_questions:
- question: >-
    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)?
- question: >-
    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?
suggested_experiments:
- description: >-
    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.
- description: >-
    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.