id: P30084
gene_symbol: ECHS1
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  ECHS1 (short-chain enoyl-CoA hydratase 1; mitochondrial enoyl-CoA hydratase, the classic
  "crotonase"; EC 4.2.1.17) is a soluble homohexameric (dimer of trimers) enzyme of the
  mitochondrial matrix that catalyzes the second step of the fatty acid beta-oxidation
  spiral: the reversible addition of water across the double bond of a 2-trans-enoyl-CoA to
  yield the corresponding (3S)-3-hydroxyacyl-CoA. It hydrates short- and medium-chain enoyl-CoA
  thioesters (C4 up to C16) with highest catalytic efficiency toward crotonyl-CoA. Beyond
  fatty acid oxidation, ECHS1 has a broad substrate range that places it at a central node of
  branched-chain amino acid catabolism: it hydrates valine-pathway intermediates (methacrylyl-CoA
  to 3-hydroxyisobutyryl-CoA, and acryloyl-CoA), 3-methylcrotonyl-CoA (leucine pathway) and
  tiglyl-CoA (isoleucine pathway). A slower delta(3)-delta(2)-enoyl-CoA isomerase activity has
  been inferred by similarity to orthologs. ECHS1 is synthesized with a cleaved N-terminal
  mitochondrial targeting presequence and is most abundant in liver, muscle and fibroblasts.
  Biallelic loss-of-function variants cause mitochondrial short-chain enoyl-CoA hydratase 1
  deficiency (ECHS1D), a Leigh-like encephalopathy in which neurotoxicity is attributed chiefly
  to accumulation of reactive valine-pathway intermediates (methacrylyl-CoA/acryloyl-CoA) rather
  than to the block in fatty acid oxidation per se.
existing_annotations:
# --- 1: mitochondrion (IBA) ---
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      Phylogenetic (IBA) localization to the mitochondrion. ECHS1 is a well-established
      mitochondrial matrix enzyme, so this is correct but less specific than the matrix
      annotations.
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct compartment but subsumed by the more precise mitochondrial matrix annotations
      (GO:0005759), which better capture where this soluble enzyme acts.
# --- 2: fatty acid beta-oxidation (IBA) ---
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Phylogenetic inference that ECHS1 participates in fatty acid beta-oxidation, consistent
      with its experimentally demonstrated role as the hydratase of the beta-oxidation spiral.
    action: ACCEPT
    reason: >-
      ECHS1 catalyzes the second (hydration) step of mitochondrial short-/medium-chain fatty
      acid beta-oxidation. This is one of the gene's core biological processes and is also
      supported by direct experimental evidence (PMID:26251176).
    supported_by:
      - reference_id: PMID:26251176
        supporting_text: "including mitochondrial short-chain fatty acid β-oxidation"
        full_text_unavailable: true
# --- 3: catalytic activity (IEA, InterPro) ---
- term:
    id: GO:0003824
    label: catalytic activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      Root-level molecular function term from InterPro domain mapping. ECHS1 is indeed a
      catalytic enzyme, but this term is uninformative and fully subsumed by the specific
      enoyl-CoA hydratase activity annotation.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      "catalytic activity" is a high-level placeholder superseded by GO:0004300 enoyl-CoA
      hydratase activity, which is experimentally supported.
# --- 4: delta(3)-delta(2)-enoyl-CoA isomerase activity (IEA, EC) ---
- term:
    id: GO:0004165
    label: delta(3)-delta(2)-enoyl-CoA isomerase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      Secondary enoyl-CoA isomerase activity (EC 5.3.3.8) assigned electronically from the
      EC/Rhea mapping. In UniProt this activity is annotated only by similarity to the rat
      ortholog (P14604, ECO:0000250), not experimentally demonstrated for human ECHS1.
    action: KEEP_AS_NON_CORE
    reason: >-
      Plausible minor activity ("At a lower rate than the hydratase reaction, catalyzes the
      isomerase reaction"), but inferred by similarity rather than measured in human, so it
      should not be treated as a core function.
    supported_by:
      - reference_id: PMID:9073515
        supporting_text: "short chain enoyl-CoA hydratase (ECHS1; EC 4.2.1.17)"
        full_text_unavailable: true
# --- 5: enoyl-CoA hydratase activity (IEA, EC/ARBA) ---
- term:
    id: GO:0004300
    label: enoyl-CoA hydratase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      Electronic assignment of the defining EC 4.2.1.17 activity. This is the core molecular
      function of ECHS1 and is independently confirmed by direct experimental data.
    action: ACCEPT
    reason: >-
      Enoyl-CoA hydratase activity is the central, experimentally validated function of ECHS1
      (PMID:26251176); the electronic annotation is correct.
    supported_by:
      - reference_id: PMID:26251176
        supporting_text: "Human ECHS1 catalyses the hydration of five substrates via different metabolic pathways"
        full_text_unavailable: true
# --- 6: mitochondrial matrix (IEA) ---
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: located_in
  review:
    summary: >-
      Electronic localization to the mitochondrial matrix, the correct compartment for this
      soluble matrix enzyme, consistent with experimental (IDA) evidence.
    action: ACCEPT
    reason: >-
      ECHS1 is a soluble homohexamer of the mitochondrial matrix (UniProt SUBCELLULAR
      LOCATION); directly supported by IDA evidence (PMID:40056416).
# --- 7: branched-chain amino acid catabolic process (IEA, ARBA) ---
- term:
    id: GO:0009083
    label: branched-chain amino acid catabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: >-
      Electronic assignment that ECHS1 acts in branched-chain amino acid catabolism. ECHS1
      hydrates valine- (methacrylyl-CoA), leucine- (3-methylcrotonyl-CoA) and isoleucine-
      (tiglyl-CoA) pathway intermediates, so this is correct.
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct, but it is the broad parent of the more specific and experimentally supported
      L-valine catabolic process (GO:0006574). Retained as a valid non-core annotation.
    supported_by:
      - reference_id: PMID:26251176
        supporting_text: "branched-chain amino acid catabolic pathways"
        full_text_unavailable: true
# --- 8: 3-hydroxyacyl-CoA dehydratase activity (IEA, RHEA) ---
- term:
    id: GO:0018812
    label: 3-hydroxyacyl-CoA dehydratase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000116
  qualifier: enables
  review:
    summary: >-
      RHEA-based assignment (RHEA:16105 etc.) describing the EC 4.2.1.17 reaction written in
      the dehydratase direction. This is the same chemistry as enoyl-CoA hydratase activity.
    action: KEEP_AS_NON_CORE
    reason: >-
      Describes the same reversible reaction as the core GO:0004300 annotation, just in the
      opposite direction; valid but redundant with the hydratase MF.
# --- 9: 3-hydroxypropionyl-CoA dehydratase activity (IEA, RHEA) ---
- term:
    id: GO:0043956
    label: 3-hydroxypropionyl-CoA dehydratase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000116
  qualifier: enables
  review:
    summary: >-
      RHEA assignment for hydration/dehydration of acryloyl-CoA (3-hydroxypropanoyl-CoA <=>
      acryloyl-CoA + H2O). Acryloyl-CoA is in the experimentally measured substrate panel,
      so this specific activity is supported (and is duplicated below by an IDA annotation).
    action: ACCEPT
    reason: >-
      ECHS1 hydrates acryloyl-CoA (a valine-pathway intermediate); experimental kinetics
      (KM=34.04 uM) and an IDA annotation (PMID:26251176) support this specific activity.
# --- 10: (2E)-butenoyl-CoA hydratase activity (IEA, RHEA) ---
- term:
    id: GO:0120092
    label: (2E)-butenoyl-CoA hydratase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000116
  qualifier: enables
  review:
    summary: >-
      RHEA assignment for hydration of crotonyl-CoA ((2E)-butenoyl-CoA), the highest-affinity
      and best characterized substrate of ECHS1.
    action: ACCEPT
    reason: >-
      Crotonyl-CoA hydration is the prototypic ECHS1 ("crotonase") reaction, with the highest
      measured catalytic specificity (KM=12.75 uM); a valid specific child of enoyl-CoA
      hydratase activity.
    supported_by:
      - reference_id: PMID:26251176
        supporting_text: "with the highest specificity for crotonyl-CoA"
        full_text_unavailable: true
# --- 11: L-amino acid catabolic process (IEA, ARBA) ---
- term:
    id: GO:0170035
    label: L-amino acid catabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: >-
      Very broad ARBA-derived process term. ECHS1's amino-acid-related role is specifically in
      branched-chain (valine) catabolism; this generic parent adds no information.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Overly general; superseded by GO:0009083 (branched-chain amino acid catabolic process)
      and GO:0006574 (L-valine catabolic process).
# --- 12: protein binding (IPI, STAT3) ---
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:23416296
  qualifier: enables
  review:
    summary: >-
      IPI annotation capturing the ECHS1-STAT3 interaction (yeast two-hybrid, GST-pulldown,
      co-IP), reported to negatively regulate STAT3 signaling. The interaction is real but the
      bare "protein binding" term is uninformative about function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Valid experimental interaction but "protein binding" conveys no specific molecular
      function; possible moonlighting regulatory role, not the metabolic core function.
    supported_by:
      - reference_id: PMID:23416296
        supporting_text: "we identified enoyl-CoA hydratase short chain 1 (ECHS1) as a novel STAT3 binding protein"
# --- 13: protein binding (IPI, LRRK2) ---
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:24510904
  qualifier: enables
  review:
    summary: >-
      IPI annotation from an unbiased LRRK2 interactor screen in which ECHS1 appeared as a hit.
      No dedicated functional follow-up establishes a metabolic role for this interaction.
    action: KEEP_AS_NON_CORE
    reason: >-
      Bare "protein binding" from a large-scale interactome screen; uninformative and not a
      core function.
# --- 14: protein binding (IPI, LRRK2) ---
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:24947832
  qualifier: enables
  review:
    summary: >-
      IPI annotation from a LRRK1/LRRK2 differential interactome study listing ECHS1 as an
      interactor.
    action: KEEP_AS_NON_CORE
    reason: >-
      Uninformative "protein binding" from an interactome dataset; retained but non-core.
# --- 15: protein binding (IPI, LRRK2) ---
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:31046837
  qualifier: enables
  review:
    summary: >-
      IPI annotation associated with a study of LRRK2-G2019S/SERCA-mediated ER stress in
      astrocytes; ECHS1 is recorded as a LRRK2 interactor.
    action: KEEP_AS_NON_CORE
    reason: >-
      Uninformative "protein binding"; no specific molecular function for ECHS1 is established.
# --- 16: L-valine catabolic process (IEA, Ensembl ortholog) ---
- term:
    id: GO:0006574
    label: L-valine catabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Orthology-based (Ensembl Compara) transfer of L-valine catabolic process. ECHS1 hydrates
      the valine-pathway intermediate methacrylyl-CoA, and its deficiency is defined as an
      inborn error of valine metabolism.
    action: ACCEPT
    reason: >-
      A core biological process for ECHS1; also supported by direct experimental (IMP) evidence
      (PMID:40056416) and by the disease phenotype (an inborn error affecting valine metabolism).
    supported_by:
      - reference_id: PMID:26251176
        supporting_text: "harbouring defective valine catabolic and β-oxidation pathways"
        full_text_unavailable: true
# --- 17: fatty acid beta-oxidation (IEA, ARBA/UniPathway) ---
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  review:
    summary: >-
      Electronic assignment of fatty acid beta-oxidation, consistent with the core function
      and with experimental evidence.
    action: ACCEPT
    reason: >-
      ECHS1 is the hydratase of the short/medium-chain beta-oxidation spiral; duplicate of the
      experimentally supported BP annotation.
# --- 18-22: fatty acid beta-oxidation (TAS, Reactome beta-ox steps) ---
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77310
  qualifier: involved_in
  review:
    summary: >-
      Reactome (TAS) annotation placing ECHS1 in the beta-oxidation of lauroyl-CoA to
      decanoyl-CoA. Correct pathway membership; one of several chain-length-specific Reactome
      steps redundant with the core BP annotation.
    action: ACCEPT
    reason: >-
      Accurately reflects ECHS1's role in the fatty acid beta-oxidation pathway.
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77346
  qualifier: involved_in
  review:
    summary: >-
      Reactome (TAS) annotation for beta-oxidation of decanoyl-CoA to octanoyl-CoA.
    action: ACCEPT
    reason: >-
      Correct pathway membership; redundant with the core fatty acid beta-oxidation annotation.
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77348
  qualifier: involved_in
  review:
    summary: >-
      Reactome (TAS) annotation for beta-oxidation of octanoyl-CoA to hexanoyl-CoA.
    action: ACCEPT
    reason: >-
      Correct pathway membership; redundant with the core fatty acid beta-oxidation annotation.
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77350
  qualifier: involved_in
  review:
    summary: >-
      Reactome (TAS) annotation for beta-oxidation of hexanoyl-CoA to butanoyl-CoA.
    action: ACCEPT
    reason: >-
      Correct pathway membership; redundant with the core fatty acid beta-oxidation annotation.
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77352
  qualifier: involved_in
  review:
    summary: >-
      Reactome (TAS) annotation for beta-oxidation of butanoyl-CoA to acetyl-CoA (the
      shortest-chain step, with crotonyl-CoA as the enoyl-CoA substrate).
    action: ACCEPT
    reason: >-
      Correct pathway membership; this final short-chain step uses crotonyl-CoA, ECHS1's best
      substrate. Redundant with the core fatty acid beta-oxidation annotation.
# --- 23: branched-chain amino acid catabolic process (TAS, Reactome) ---
- term:
    id: GO:0009083
    label: branched-chain amino acid catabolic process
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-70895
  qualifier: involved_in
  review:
    summary: >-
      Reactome (TAS) placement of ECHS1 in branched-chain amino acid catabolism, consistent
      with its hydration of valine/leucine/isoleucine pathway intermediates.
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct but broad; the specific valine catabolism term is the more informative core BP.
# --- 24: enoyl-CoA hydratase activity (EXP, PMID:26251176) ---
- term:
    id: GO:0004300
    label: enoyl-CoA hydratase activity
  evidence_type: EXP
  original_reference_id: PMID:26251176
  qualifier: enables
  review:
    summary: >-
      Experimental (EXP) annotation of the defining enoyl-CoA hydratase activity, based on
      purified human ECHS1 assayed against multiple enoyl-CoA substrates.
    action: ACCEPT
    reason: >-
      Direct experimental demonstration of the core molecular function of ECHS1.
    supported_by:
      - reference_id: PMID:26251176
        supporting_text: "we purified human ECHS1, and determined the substrate specificity of ECHS1 for five substrates via different metabolic pathways"
        full_text_unavailable: true
# --- 25-30: enoyl-CoA hydratase activity (TAS, Reactome reactions) ---
- term:
    id: GO:0004300
    label: enoyl-CoA hydratase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77256
  qualifier: enables
  review:
    summary: >-
      Reactome (TAS) annotation of enoyl-CoA hydratase activity for a specific beta-oxidation
      reaction (2-trans-dodecenoyl-CoA hydration).
    action: ACCEPT
    reason: >-
      Correct molecular function; one of several Reactome reaction-level annotations redundant
      with the experimentally supported core MF.
- term:
    id: GO:0004300
    label: enoyl-CoA hydratase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77314
  qualifier: enables
  review:
    summary: >-
      Reactome (TAS) enoyl-CoA hydratase activity for crotonoyl-CoA hydration.
    action: ACCEPT
    reason: >-
      Correct molecular function; redundant with the core enoyl-CoA hydratase annotation.
- term:
    id: GO:0004300
    label: enoyl-CoA hydratase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77325
  qualifier: enables
  review:
    summary: >-
      Reactome (TAS) enoyl-CoA hydratase activity for trans-hex-2-enoyl-CoA hydration.
    action: ACCEPT
    reason: >-
      Correct molecular function; redundant with the core enoyl-CoA hydratase annotation.
- term:
    id: GO:0004300
    label: enoyl-CoA hydratase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77333
  qualifier: enables
  review:
    summary: >-
      Reactome (TAS) enoyl-CoA hydratase activity for trans-oct-2-enoyl-CoA hydration.
    action: ACCEPT
    reason: >-
      Correct molecular function; redundant with the core enoyl-CoA hydratase annotation.
- term:
    id: GO:0004300
    label: enoyl-CoA hydratase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77344
  qualifier: enables
  review:
    summary: >-
      Reactome (TAS) enoyl-CoA hydratase activity for trans-dec-2-enoyl-CoA hydration.
    action: ACCEPT
    reason: >-
      Correct molecular function; redundant with the core enoyl-CoA hydratase annotation.
- term:
    id: GO:0004300
    label: enoyl-CoA hydratase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9916717
  qualifier: enables
  review:
    summary: >-
      Reactome (TAS) enoyl-CoA hydratase activity within the ECHS1-deficiency disease pathway
      (synthesis of beta-hydroxyisobutyryl-CoA from methacrylyl-CoA in valine catabolism).
    action: ACCEPT
    reason: >-
      Correct molecular function applied in the valine-catabolism context; redundant with the
      core enoyl-CoA hydratase annotation.
# --- 31: L-lysine catabolic process (IMP, PMID:37198486) ---
- term:
    id: GO:0019477
    label: L-lysine catabolic process
  evidence_type: IMP
  original_reference_id: PMID:37198486
  qualifier: involved_in
  review:
    summary: >-
      IMP annotation derived from a glioma study showing that ECHS1 is the crotonyl-CoA
      hydratase whose downregulation accumulates crotonyl-CoA (a lysine-catabolism intermediate
      produced via GCDH) and drives histone H4 lysine crotonylation. ECHS1 consumes crotonyl-CoA
      rather than performing a dedicated lysine-degradation step, so this placement reflects its
      action on a shared crotonyl-CoA pool.
    action: KEEP_AS_NON_CORE
    reason: >-
      Curator-assigned from experimental (full-text) evidence; deferred to per guidelines.
      Retained as non-core because ECHS1's connection to lysine catabolism is via the shared
      crotonyl-CoA metabolite, not a canonical lysine-degradation reaction.
    supported_by:
      - reference_id: PMID:37198486
        supporting_text: "downregulation of the crotonyl-CoA hydratase enoyl-CoA hydratase short chain 1 \n(ECHS1), leading to accumulation of intracellular crotonyl-CoA and histone H4 \nlysine crotonylation"
# --- 32: mitochondrion (IDA, HPA) ---
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  qualifier: located_in
  review:
    summary: >-
      Immunofluorescence-based (IDA, HPA) mitochondrial localization. Correct but less precise
      than the matrix annotation.
    action: KEEP_AS_NON_CORE
    reason: >-
      Subsumed by the more specific mitochondrial matrix localization.
# --- 33: mitochondrial matrix (IDA, PMID:40056416) ---
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: IDA
  original_reference_id: PMID:40056416
  qualifier: located_in
  review:
    summary: >-
      Direct experimental (IDA) localization of ECHS1 to the mitochondrial matrix, the precise
      compartment for this soluble homohexameric enzyme.
    action: ACCEPT
    reason: >-
      Best-supported and most specific subcellular localization; this is the core location of
      ECHS1.
# --- 34: L-valine catabolic process (IMP, PMID:40056416) ---
- term:
    id: GO:0006574
    label: L-valine catabolic process
  evidence_type: IMP
  original_reference_id: PMID:40056416
  qualifier: involved_in
  review:
    summary: >-
      Direct experimental (IMP) evidence that ECHS1 acts in valine catabolism: its loss (like
      loss of the downstream enzyme HIBCH) elevates lysine methacrylation, reflecting build-up
      of the valine-pathway intermediate methacrylyl-CoA that ECHS1 normally hydrates.
    action: ACCEPT
    reason: >-
      A core biological process of ECHS1, supported by genetic loss-of-function evidence and
      consistent with ECHS1 deficiency being an inborn error of valine metabolism.
    supported_by:
      - reference_id: PMID:40056416
        supporting_text: "Elevated lysine methacrylation (Kmea) is observed in both HIBCH- and ECHS1-deficient cells and \nfly tissues"
# --- 35: 3-hydroxypropionyl-CoA dehydratase activity (IDA, PMID:26251176) ---
- term:
    id: GO:0043956
    label: 3-hydroxypropionyl-CoA dehydratase activity
  evidence_type: IDA
  original_reference_id: PMID:26251176
  qualifier: enables
  review:
    summary: >-
      Direct experimental (IDA) annotation of acryloyl-CoA hydration / 3-hydroxypropionyl-CoA
      dehydration, one of the five substrate reactions measured for purified human ECHS1.
    action: ACCEPT
    reason: >-
      Experimentally measured specific activity (acryloyl-CoA, KM=34.04 uM); a valid specific
      child of enoyl-CoA hydratase activity relevant to valine/propionate metabolism.
    supported_by:
      - reference_id: PMID:26251176
        supporting_text: "Human ECHS1 catalyses the hydration of five substrates via different metabolic pathways"
        full_text_unavailable: true
# --- 36: mitochondrial matrix (TAS, Reactome) ---
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9916717
  qualifier: located_in
  review:
    summary: >-
      Reactome (TAS) mitochondrial matrix localization within the ECHS1-deficiency pathway.
    action: ACCEPT
    reason: >-
      Correct, specific localization; consistent with the IDA evidence.
# --- 37: mitochondrion (HTP, PMID:34800366) ---
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HTP
  original_reference_id: PMID:34800366
  qualifier: located_in
  review:
    summary: >-
      High-throughput (HTP) detection of ECHS1 in a high-confidence human mitochondrial
      proteome. Confirms mitochondrial localization at lower specificity than the matrix term.
    action: KEEP_AS_NON_CORE
    reason: >-
      Supports mitochondrial localization but is subsumed by the matrix annotation.
# --- 38: enoyl-CoA hydratase activity (IDA, PMID:26251176) ---
- term:
    id: GO:0004300
    label: enoyl-CoA hydratase activity
  evidence_type: IDA
  original_reference_id: PMID:26251176
  qualifier: enables
  review:
    summary: >-
      Direct experimental (IDA) demonstration of enoyl-CoA hydratase activity using purified
      human ECHS1, the strongest evidence for the gene's core molecular function.
    action: ACCEPT
    reason: >-
      Definitive experimental support for the core enoyl-CoA hydratase activity.
    supported_by:
      - reference_id: PMID:26251176
        supporting_text: "we purified human ECHS1, and determined the substrate specificity of ECHS1 for five substrates"
        full_text_unavailable: true
# --- 39: fatty acid beta-oxidation (IDA, PMID:26251176) ---
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: IDA
  original_reference_id: PMID:26251176
  qualifier: involved_in
  review:
    summary: >-
      Direct experimental (IDA) evidence for ECHS1's role in fatty acid beta-oxidation, based
      on hydratase activity toward beta-oxidation enoyl-CoA substrates and the deficiency
      phenotype affecting the beta-oxidation pathway.
    action: ACCEPT
    reason: >-
      A core biological process; experimentally supported.
    supported_by:
      - reference_id: PMID:26251176
        supporting_text: "including mitochondrial short-chain fatty acid β-oxidation"
        full_text_unavailable: true
# --- 40-43: mitochondrial matrix (TAS, Reactome) ---
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-70870
  qualifier: located_in
  review:
    summary: >-
      Reactome (TAS) mitochondrial matrix localization (methacrylyl-CoA hydration reaction).
    action: ACCEPT
    reason: >-
      Correct, specific localization; consistent with experimental evidence.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77256
  qualifier: located_in
  review:
    summary: >-
      Reactome (TAS) mitochondrial matrix localization (a beta-oxidation hydration reaction).
    action: ACCEPT
    reason: >-
      Correct, specific localization; redundant with other matrix annotations.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77314
  qualifier: located_in
  review:
    summary: >-
      Reactome (TAS) mitochondrial matrix localization (crotonoyl-CoA hydration reaction).
    action: ACCEPT
    reason: >-
      Correct, specific localization; redundant with other matrix annotations.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77325
  qualifier: located_in
  review:
    summary: >-
      Reactome (TAS) mitochondrial matrix localization (hex-2-enoyl-CoA hydration reaction).
    action: ACCEPT
    reason: >-
      Correct, specific localization; redundant with other matrix annotations.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77333
  qualifier: located_in
  review:
    summary: >-
      Reactome (TAS) mitochondrial matrix localization (oct-2-enoyl-CoA hydration reaction).
    action: ACCEPT
    reason: >-
      Correct, specific localization; redundant with other matrix annotations.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77344
  qualifier: located_in
  review:
    summary: >-
      Reactome (TAS) mitochondrial matrix localization (dec-2-enoyl-CoA hydration reaction).
    action: ACCEPT
    reason: >-
      Correct, specific localization; redundant with other matrix annotations.
# --- 44: protein binding (IPI, AIP) ---
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:14557246
  qualifier: enables
  review:
    summary: >-
      IPI annotation from a study of the mitochondrial import mediator AIP (which binds Tom20
      and preproteins). ECHS1 features as a mitochondrial import substrate/preprotein rather
      than a functional partner.
    action: KEEP_AS_NON_CORE
    reason: >-
      Uninformative "protein binding"; reflects ECHS1's status as an imported matrix preprotein,
      not a molecular function.
# --- 45: mitochondrion (TAS, PMID:16130169) ---
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: TAS
  original_reference_id: PMID:16130169
  qualifier: located_in
  review:
    summary: >-
      TAS mitochondrial localization from a HUVEC proteomics study. Correct compartment, low
      specificity.
    action: KEEP_AS_NON_CORE
    reason: >-
      Subsumed by the more specific mitochondrial matrix localization.
# --- 46: enoyl-CoA hydratase activity (TAS, PMID:9073515) ---
- term:
    id: GO:0004300
    label: enoyl-CoA hydratase activity
  evidence_type: TAS
  original_reference_id: PMID:9073515
  qualifier: enables
  review:
    summary: >-
      TAS annotation of enoyl-CoA hydratase activity from the gene-cloning paper, which
      describes ECHS1 as catalyzing the second step of beta-oxidation (EC 4.2.1.17).
    action: ACCEPT
    reason: >-
      Correct core molecular function; consistent with the experimental IDA/EXP evidence.
    supported_by:
      - reference_id: PMID:9073515
        supporting_text: "is catalyzed by short \nchain enoyl-CoA hydratase (ECHS1; EC 4.2.1.17)"
        full_text_unavailable: true
# --- 47: fatty acid beta-oxidation (TAS, PMID:9073515) ---
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: TAS
  original_reference_id: PMID:9073515
  qualifier: involved_in
  review:
    summary: >-
      TAS annotation of fatty acid beta-oxidation from the cloning paper, which identifies
      ECHS1 as catalyzing the second step of mitochondrial fatty acid beta-oxidation.
    action: ACCEPT
    reason: >-
      Correct core biological process; consistent with experimental evidence.
    supported_by:
      - reference_id: PMID:9073515
        supporting_text: "The second step in mitochondrial fatty acid beta-oxidation is catalyzed by short"
        full_text_unavailable: true
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:0000052
  title: Gene Ontology annotation based on curation of immunofluorescence data
  findings: []
- id: GO_REF:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data to
    orthologs using Ensembl Compara
  findings: []
- id: GO_REF:0000116
  title: Automatic Gene Ontology annotation based on Rhea 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:14557246
  title: AIP is a mitochondrial import mediator that binds to both import receptor
    Tom20 and preproteins.
  findings:
    - statement: >-
        ECHS1 appears in this study as a model imported mitochondrial preprotein/matrix
        protein; the AIP-Tom20-preprotein system mediates mitochondrial protein import.
      supporting_text: >-
        AIP is a mitochondrial import mediator that binds to both import receptor Tom20
      full_text_unavailable: true
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Correctly cited but pertains to mitochondrial protein import machinery; ECHS1 is a
      preprotein substrate here, not a functional partner. Supports only the uninformative
      "protein binding" annotation.
- id: PMID:16130169
  title: Proteomics of human umbilical vein endothelial cells applied to etoposide-induced
    apoptosis.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Proteomics survey; supports only generic mitochondrial localization of ECHS1.
- id: PMID:23416296
  title: ECHS1 interacts with STAT3 and negatively regulates STAT3 signaling.
  findings:
    - statement: >-
        ECHS1 was identified as a STAT3-binding protein that represses STAT3 activity by
        inhibiting STAT3 phosphorylation, suggesting a possible regulatory/moonlighting role.
      supporting_text: >-
        we identified enoyl-CoA hydratase short chain 1 (ECHS1) as a novel STAT3 binding protein
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Abstract-only; interaction supported by Y2H, GST-pulldown and co-IP. Supports a
      non-core STAT3-regulatory interaction, not the metabolic core function.
- id: PMID:24510904
  title: Unbiased screen for interactors of leucine-rich repeat kinase 2 supports
    a common pathway for sporadic and familial Parkinson disease.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Large-scale LRRK2 interactor screen; ECHS1 is one hit. Supports only "protein binding".
- id: PMID:24947832
  title: Differential protein-protein interactions of LRRK1 and LRRK2 indicate roles
    in distinct cellular signaling pathways.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      LRRK1/LRRK2 interactome dataset; supports only "protein binding".
- id: PMID:26251176
  title: 'Clinical, biochemical and metabolic characterisation of a mild form of human
    short-chain enoyl-CoA hydratase deficiency: significance of increased N-acetyl-S-(2-carboxypropyl)cysteine
    excretion.'
  findings:
    - statement: >-
        Purified human ECHS1 hydrates five enoyl-CoA substrates across different metabolic
        pathways, with highest specificity for crotonyl-CoA and lowest for tiglyl-CoA,
        spanning fatty acid beta-oxidation and branched-chain amino acid catabolism.
      supporting_text: >-
        Human ECHS1 catalyses the hydration of five substrates via different metabolic
        pathways, with the highest specificity for crotonyl-CoA and the lowest specificity
        for tiglyl-CoA.
      full_text_unavailable: true
    - statement: >-
        ECHS1 deficiency impairs both valine catabolic and beta-oxidation pathways; affected
        patients excrete N-acetyl-S-(2-carboxypropyl)cysteine, a methacrylyl-CoA metabolite.
      supporting_text: >-
        harbouring defective valine catabolic and β-oxidation pathways
      full_text_unavailable: true
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Key functional/biochemical characterization of human ECHS1 (purified enzyme, substrate
      specificity, KM/Vmax). Abstract-only in cache; underpins the EXP/IDA core annotations.
- id: PMID:31046837
  title: Parkinson's disease-associated LRRK2-G2019S mutant acts through regulation
    of SERCA activity to control ER stress in astrocytes.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      LRRK2/SERCA/ER-stress study; supports only an ECHS1-LRRK2 "protein binding" record.
- id: PMID:34800366
  title: Quantitative high-confidence human mitochondrial proteome and its dynamics
    in cellular context.
  findings:
    - statement: >-
        ECHS1 is part of the high-confidence human mitochondrial proteome.
      supporting_text: >-
        Quantitative high-confidence human mitochondrial proteome and its dynamics
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      High-throughput proteomic confirmation of mitochondrial localization.
- id: PMID:37198486
  title: Lysine catabolism reprograms tumour immunity through histone crotonylation.
  findings:
    - statement: >-
        ECHS1 is the crotonyl-CoA hydratase; its downregulation accumulates crotonyl-CoA
        (a lysine-catabolism intermediate) and increases histone H4 lysine crotonylation.
      supporting_text: >-
        downregulation of the crotonyl-CoA hydratase enoyl-CoA hydratase short chain 1
        (ECHS1), leading to accumulation of intracellular crotonyl-CoA and histone H4
        lysine crotonylation
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Full text available; basis for the FlyBase IMP to L-lysine catabolic process. ECHS1's
      link to lysine catabolism is through consumption of the shared crotonyl-CoA pool.
- id: PMID:40056416
  title: Ectopic protein lysine methacrylation contributes to defects caused by loss
    of HIBCH or ECHS1.
  findings:
    - statement: >-
        Loss of ECHS1 (or downstream HIBCH) elevates lysine methacrylation and causes
        abnormal mitochondrial morphology and respiratory defects, consistent with build-up
        of the valine-pathway intermediate methacrylyl-CoA that ECHS1 normally hydrates.
      supporting_text: >-
        Elevated lysine methacrylation (Kmea) is observed in both HIBCH- and ECHS1-deficient
        cells and
        fly tissues
      full_text_unavailable: true
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Abstract-only; basis for the IMP annotations to L-valine catabolic process and
      mitochondrial matrix localization. Mechanistically links ECHS1 loss to valine-pathway
      intermediate accumulation.
- id: PMID:9073515
  title: 'Human mitochondrial enoyl-CoA hydratase gene (ECHS1): structural organization
    and assignment to chromosome 10q26.2-q26.3.'
  findings:
    - statement: >-
        ECHS1 (EC 4.2.1.17) catalyzes the second step of mitochondrial fatty acid
        beta-oxidation; the gene maps to chromosome 10q26.2-q26.3.
      supporting_text: >-
        The second step in mitochondrial fatty acid beta-oxidation is catalyzed by short
      full_text_unavailable: true
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Original human ECHS1 gene characterization; abstract-only. Establishes EC 4.2.1.17 and
      beta-oxidation role.
- id: Reactome:R-HSA-70870
  title: ECHS1 hydrates methacrylyl-CoA
  findings: []
- id: Reactome:R-HSA-70895
  title: Branched-chain amino acid catabolism
  findings: []
- id: Reactome:R-HSA-77256
  title: 2-trans-Dodecenoyl-CoA+H2O =>( S)-3-Hydroxydodecanoyl-CoA
  findings: []
- id: Reactome:R-HSA-77310
  title: Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA
  findings: []
- id: Reactome:R-HSA-77314
  title: Crotonoyl-CoA+H2O => (S)-3-Hydroxybutanoyl-CoA
  findings: []
- id: Reactome:R-HSA-77325
  title: trans-Hex-2-enoyl-CoA+H2O<=>(S)-Hydroxyhexanoyl-CoA
  findings: []
- id: Reactome:R-HSA-77333
  title: trans-Oct-2-enoyl-CoA+H2O => (S)-Hydroxyoctanoyl-CoA
  findings: []
- id: Reactome:R-HSA-77344
  title: trans-Dec-2-enoyl-CoA+H2O => (S)-Hydroxydecanoyl-CoA
  findings: []
- id: Reactome:R-HSA-77346
  title: Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA
  findings: []
- id: Reactome:R-HSA-77348
  title: Beta oxidation of octanoyl-CoA to hexanoyl-CoA
  findings: []
- id: Reactome:R-HSA-77350
  title: Beta oxidation of hexanoyl-CoA to butanoyl-CoA
  findings: []
- id: Reactome:R-HSA-77352
  title: Beta oxidation of butanoyl-CoA to acetyl-CoA
  findings: []
- id: Reactome:R-HSA-9916717
  title: ECHS1 mutants don't synthesize beta-hydroxyisobutyryl-CoA
  findings: []
core_functions:
- description: >-
    Catalyzes the second step of the mitochondrial fatty acid beta-oxidation spiral: the
    reversible hydration of short- and medium-chain 2-trans-enoyl-CoA thioesters (C4-C16) to
    the corresponding (3S)-3-hydroxyacyl-CoA, with highest catalytic efficiency toward
    crotonyl-CoA.
  supported_by:
    - reference_id: PMID:26251176
      supporting_text: >-
        Human ECHS1 catalyses the hydration of five substrates via different metabolic
        pathways, with the highest specificity for crotonyl-CoA and the lowest specificity
        for tiglyl-CoA.
      full_text_unavailable: true
    - reference_id: PMID:9073515
      supporting_text: >-
        The second step in mitochondrial fatty acid beta-oxidation is catalyzed by short
      full_text_unavailable: true
  molecular_function:
    id: GO:0004300
    label: enoyl-CoA hydratase activity
  directly_involved_in:
    - id: GO:0006635
      label: fatty acid beta-oxidation
  locations:
    - id: GO:0005759
      label: mitochondrial matrix
- description: >-
    Hydrates branched-chain amino acid catabolic intermediates, most importantly the
    valine-pathway intermediate methacrylyl-CoA (to (S)-3-hydroxyisobutyryl-CoA) and
    acryloyl-CoA; this detoxifying step links ECHS1 to valine catabolism, and its failure in
    ECHS1 deficiency causes accumulation of reactive valine-pathway thioesters.
  supported_by:
    - reference_id: PMID:26251176
      supporting_text: >-
        harbouring defective valine catabolic and β-oxidation pathways
      full_text_unavailable: true
    - reference_id: PMID:40056416
      supporting_text: >-
        Elevated lysine methacrylation (Kmea) is observed in both HIBCH- and ECHS1-deficient
        cells and
        fly tissues
      full_text_unavailable: true
  molecular_function:
    id: GO:0043956
    label: 3-hydroxypropionyl-CoA dehydratase activity
  directly_involved_in:
    - id: GO:0006574
      label: L-valine catabolic process
  locations:
    - id: GO:0005759
      label: mitochondrial matrix
proposed_new_terms: []
suggested_questions:
- question: >-
    Is ECHS1's reported negative regulation of STAT3 signaling (PMID:23416296) a genuine
    moonlighting function distinct from its hydratase activity, and does it occur outside the
    mitochondrial matrix?
- question: >-
    Should the L-lysine catabolic process annotation (GO:0019477) be retained, given that
    ECHS1's connection to lysine catabolism is via consumption of the shared crotonyl-CoA
    pool rather than a dedicated lysine-degradation reaction?
- question: >-
    To what extent is ECHS1 deficiency neurotoxicity driven by accumulation of reactive
    valine-pathway intermediates (methacrylyl-CoA/acryloyl-CoA) and ectopic protein lysine
    methacrylation versus the loss of beta-oxidation flux?
suggested_experiments:
- description: >-
    Measure in vitro hydratase kinetics of purified recombinant human ECHS1 against the full
    panel of branched-chain enoyl-CoA substrates (methacrylyl-CoA, 3-methylcrotonyl-CoA,
    tiglyl-CoA, acryloyl-CoA) alongside crotonyl-CoA to quantify its relative contribution to
    each amino acid catabolic pathway.
  hypothesis: >-
    ECHS1 is the principal short-chain enoyl-CoA hydratase for valine-pathway intermediates,
    explaining why its deficiency presents primarily as an inborn error of valine metabolism.
- description: >-
    In ECHS1-null cells and patient fibroblasts, perform metabolomic tracing of valine and
    fatty-acid carbon to determine which accumulating thioester (methacrylyl-CoA vs
    acryloyl-CoA) most strongly correlates with mitochondrial dysfunction and protein
    methacrylation.
  hypothesis: >-
    Accumulation of methacrylyl-CoA and consequent ectopic lysine methacrylation, rather than
    the beta-oxidation block, is the principal driver of the ECHS1-deficiency phenotype.
- description: >-
    Test whether the slower delta(3)-delta(2)-enoyl-CoA isomerase activity inferred by
    similarity is detectable for purified human ECHS1 using 3-enoyl-CoA substrates.
  hypothesis: >-
    Human ECHS1 retains a low-level enoyl-CoA isomerase activity analogous to its rodent
    ortholog, supporting the EC 5.3.3.8 annotation.