id: Q16836
gene_symbol: HADH
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  HADH (Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial; also known as SCHAD, HAD1,
  M/SCHAD) is a soluble mitochondrial matrix enzyme that catalyzes the third step of the
  fatty-acid beta-oxidation spiral: the NAD+-dependent oxidation of L-(3S)-3-hydroxyacyl-CoA
  to 3-ketoacyl-CoA (EC 1.1.1.35). It acts as a homodimer and preferentially oxidizes short-
  and medium-chain 3-hydroxyacyl-CoA substrates (roughly C4-C10), functionally distinct from
  the long-chain, membrane-associated mitochondrial trifunctional protein alpha subunit (HADHA).
  Catalysis uses His158 as a general base assisted by Glu170. Beyond its catalytic role, HADH
  has a well-documented regulatory (moonlighting) function in pancreatic beta-cells: it binds
  and inhibits the activation of glutamate dehydrogenase 1 (GLUD1), thereby restraining
  amino-acid-stimulated insulin secretion. Loss of HADH function causes hyperinsulinaemic
  hypoglycaemia and a fatty-acid-oxidation disorder, establishing the first known link between
  beta-oxidation and dysregulated insulin secretion. HADH is expressed in liver, kidney,
  pancreatic islets, heart, skeletal muscle, and adipose tissue, and in rodents contributes to
  body-weight regulation and adaptive thermogenesis.
alternative_products:
- name: '1'
  id: Q16836-1
- name: '2'
  id: Q16836-2
  sequence_note: VSP_016551, VSP_016552
- name: '3'
  id: Q16836-3
  sequence_note: VSP_016552
existing_annotations:
- term:
    id: GO:0003857
    label: (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      Phylogenetically inferred core molecular function. This is the defining catalytic activity
      of HADH/SCHAD, directly demonstrated for the human enzyme by purified-protein biochemistry
      and crystallography and by patient-mutant expression studies. The IBA call is at the correct
      level of specificity and is strongly corroborated by experimental annotations on the same
      term.
    action: ACCEPT
    reason: >-
      Bona fide enzymatic function supported across the 3-hydroxyacyl-CoA dehydrogenase family and
      by direct human experimental data (PMID:10231530, PMID:11489939, PMID:16725361).
    supported_by:
    - reference_id: PMID:10231530
      supporting_text: "catalyzes the oxidation of the hydroxyl group of L-3-hydroxyacyl-CoA to a keto group, concomitant with the reduction of NAD+ to NADH"
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      HADH is a mitochondrial matrix enzyme, so a mitochondrial location is correct. However,
      'mitochondrion' is the generic parent of the more precise and experimentally supported
      'mitochondrial matrix' (GO:0005759). Correct but non-core; the matrix term should carry the
      core localization.
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct compartment but less specific than the supported mitochondrial matrix annotation.
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Core biological process. HADH catalyzes the third step of the mitochondrial beta-oxidation
      cycle; this is its principal pathway role, supported by enzymology, the UniProt-curated
      pathway assignment, and patient deficiency phenotypes.
    action: ACCEPT
    reason: >-
      Directly supported by experimental data and UniProt pathway curation (lipid metabolism;
      fatty acid beta-oxidation).
    supported_by:
    - reference_id: PMID:11489939
      supporting_text: "This is the first defect in fatty acid beta-oxidation that has been associated with hyperinsulinism"
- term:
    id: GO:0003857
    label: (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      Electronic (multi-method) inference of the core catalytic activity. Redundant with the
      experimental and IBA annotations on the same term and correct.
    action: ACCEPT
    reason: >-
      Same correct molecular function as the experimentally supported annotation.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: >-
      Correct and specific subcellular localization derived from the UniProt subcellular-location
      vocabulary. HADH is a soluble matrix homodimer; this is the appropriate core location term
      and is independently supported by TAS (Reactome) and high-confidence mitochondrial proteomics.
    action: ACCEPT
    reason: >-
      Matches the curated UniProt 'Mitochondrion matrix' location and is the most precise
      localization for HADH.
- term:
    id: GO:0006631
    label: fatty acid metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: >-
      Correct but generic. 'Fatty acid metabolic process' is a high-level parent of the specific
      and experimentally supported 'fatty acid beta-oxidation' (GO:0006635). Keep as non-core in
      favor of the more informative beta-oxidation term.
    action: KEEP_AS_NON_CORE
    reason: >-
      Subsumed by the more specific beta-oxidation annotation.
- term:
    id: GO:0016491
    label: oxidoreductase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      Correct but maximally generic molecular-function class. HADH is an NAD+-dependent
      oxidoreductase, but this term is a distant parent of the specific GO:0003857 activity.
    action: KEEP_AS_NON_CORE
    reason: >-
      Generic parent of the specific dehydrogenase activity; uninformative as a standalone core
      function.
- term:
    id: GO:0016509
    label: long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000116
  qualifier: enables
  review:
    summary: >-
      This Rhea-mapped annotation asserts long-chain (C16) 3-hydroxyacyl-CoA dehydrogenase
      activity. HADH is the SHORT/medium-chain enzyme (preferring C4-C10); the long-chain matrix
      activity is the dedicated function of HADHA (MTP alpha subunit). UniProt lists a long-chain
      Rhea reaction for HADH only 'By similarity' to pig liver SCHAD (P00348), not as a preferred
      human activity. Annotating HADH with the long-chain-specific term misrepresents substrate
      preference and overlaps the distinct HADHA function.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      HADH preferentially oxidizes short/medium-chain (C4-C10) 3-hydroxyacyl-CoAs; long-chain
      activity is minor/by-similarity and is the defining role of the paralog HADHA. The
      substrate-general GO:0003857 already captures the correct activity.
- term:
    id: GO:0016616
    label: oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP
      as acceptor
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      Correct but generic intermediate parent of GO:0003857. Accurately describes the chemistry
      (oxidation of a CH-OH group with NAD+ as acceptor) but is less informative than the specific
      activity term.
    action: KEEP_AS_NON_CORE
    reason: >-
      Generic parent of the specific 3-hydroxyacyl-CoA dehydrogenase activity.
- term:
    id: GO:0070403
    label: NAD+ binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      NAD+ is the cofactor for the dehydrogenase reaction and binding is documented
      crystallographically. Correct molecular detail of the catalytic mechanism; complementary to
      (and subordinate to) the core dehydrogenase activity rather than a standalone core function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Cofactor-binding activity supporting the core catalytic function; also captured by the IDA
      annotation from PMID:10840044.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: located_in
  review:
    summary: >-
      Correct mitochondrial localization by orthology transfer, but generic relative to the
      specific 'mitochondrial matrix' term.
    action: KEEP_AS_NON_CORE
    reason: >-
      Less specific than the supported mitochondrial matrix annotation.
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  review:
    summary: >-
      Electronic inference of the core beta-oxidation process, redundant with and consistent with
      the experimental (IDA) and IBA annotations on this term.
    action: ACCEPT
    reason: >-
      Correct core biological process supported by experimental evidence.
- term:
    id: GO:0009410
    label: response to xenobiotic stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Electronically transferred from a rodent ortholog (rat Q9WVK7). A generic physiological
      'response' term with no mechanistic link to HADH's molecular function; weakly informative
      and not part of the gene's core biology.
    action: KEEP_AS_NON_CORE
    reason: >-
      Orthology-transferred generic response term; not contradicted but low information and not a
      core function.
- term:
    id: GO:0009725
    label: response to hormone
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Generic 'response to hormone' transferred electronically from a rodent ortholog. Broad and
      mechanistically uninformative for HADH.
    action: KEEP_AS_NON_CORE
    reason: >-
      Orthology-transferred generic term; non-core.
- term:
    id: GO:0014823
    label: response to activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Generic physiological response term transferred from a rodent ortholog; not informative
      about HADH molecular function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Orthology-transferred generic term; non-core.
- term:
    id: GO:0032868
    label: response to insulin
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Generic 'response to insulin' transferred from a rodent ortholog. While HADH biology is
      linked to insulin (through its regulatory effect ON secretion), 'response to insulin' is a
      distinct, broad term and is mechanistically uninformative here.
    action: KEEP_AS_NON_CORE
    reason: >-
      Orthology-transferred generic response term; the relevant insulin biology is captured by the
      regulation-of-insulin-secretion annotations.
- term:
    id: GO:0046676
    label: negative regulation of insulin secretion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Captures HADH's regulatory (moonlighting) role in pancreatic beta-cells: by binding and
      inhibiting GLUD1, HADH restrains amino-acid-stimulated insulin secretion, so its loss leads
      to inappropriate insulin oversecretion (hyperinsulinism). This is the more mechanistically
      precise insulin-secretion term and is well supported by human disease and mouse knockout
      data. Genuine secondary function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Well-supported regulatory function (GDH inhibition / restraint of insulin secretion), but
      secondary to the core beta-oxidation enzymatic role.
    supported_by:
    - reference_id: PMID:21990309
      supporting_text: "insulin secretion in response to glucose and glucose plus palmitate was elevated in isolated islets of knockout mice"
- term:
    id: GO:0050796
    label: regulation of insulin secretion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Parent term of 'negative regulation of insulin secretion'. Correct and supported, but less
      precise than the negative-regulation child that matches the GDH-inhibition mechanism.
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct regulatory role but subsumed by the more specific negative-regulation term.
- term:
    id: GO:0120162
    label: positive regulation of cold-induced thermogenesis
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Based on the mouse Hadh knockout phenotype (impaired cold tolerance / adaptive
      thermogenesis). This is a downstream physiological consequence of impaired fatty-acid
      oxidation rather than a distinct molecular function of HADH; appropriate to retain as a
      non-core, organism-level process.
    action: KEEP_AS_NON_CORE
    reason: >-
      Mouse-derived physiological phenotype downstream of FAO; non-core.
    supported_by:
    - reference_id: PMID:21990309
      supporting_text: "SCHAD plays an important role in adaptive thermogenesis"
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  qualifier: located_in
  review:
    summary: >-
      Direct (immunofluorescence/HPA) evidence for mitochondrial localization. Correct; generic
      relative to the matrix sub-compartment but a valid experimental localization.
    action: KEEP_AS_NON_CORE
    reason: >-
      Experimentally supported mitochondrial localization, less specific than mitochondrial matrix.
- term:
    id: GO:0003857
    label: (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
  evidence_type: EXP
  original_reference_id: PMID:10231530
  qualifier: enables
  review:
    summary: >-
      Direct experimental demonstration of the core catalytic activity via purified recombinant
      human heart SCHAD, kinetics, and crystal structures of the enzyme with NAD+ and substrate.
      This is the strongest evidence for HADH's defining molecular function.
    action: ACCEPT
    reason: >-
      Gold-standard experimental evidence for the core dehydrogenase activity.
    supported_by:
    - reference_id: PMID:10231530
      supporting_text: "catalyzes the oxidation of the hydroxyl group of L-3-hydroxyacyl-CoA to a keto group, concomitant with the reduction of NAD+ to NADH"
- term:
    id: GO:0003857
    label: (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
  evidence_type: EXP
  original_reference_id: PMID:16725361
  qualifier: enables
  review:
    summary: >-
      Experimental support from kinetic analysis of patient-derived missense mutants (D45G with
      altered NADH Km; Y214H with no detectable activity), directly assaying the human SCHAD
      3-hydroxyacyl-CoA dehydrogenase activity.
    action: ACCEPT
    reason: >-
      Independent experimental confirmation of the core dehydrogenase activity through mutant
      enzymology.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HTP
  original_reference_id: PMID:34800366
  qualifier: located_in
  review:
    summary: >-
      High-throughput high-confidence mitochondrial proteomics confirming HADH as a mitochondrial
      protein. Correct; generic relative to the matrix term but a valid orthogonal localization
      evidence source.
    action: KEEP_AS_NON_CORE
    reason: >-
      Supports mitochondrial localization; less specific than mitochondrial matrix.
- term:
    id: GO:0050796
    label: regulation of insulin secretion
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  review:
    summary: >-
      Sequence-similarity transfer (from mouse Q61425) of HADH's regulatory role in insulin
      secretion. Reflects the GDH-inhibition moonlighting mechanism. Correct and supported, but
      less precise than the negative-regulation child term and secondary to the core enzymatic
      function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Genuine but secondary regulatory function; the negative-regulation term is more precise.
    supported_by:
    - reference_id: PMID:21990309
      supporting_text: "Blood glucose concentrations in the fasted and postprandial state were significantly lower in hadh(-/-) mice, whereas insulin levels were elevated"
- term:
    id: GO:0070403
    label: NAD+ binding
  evidence_type: IDA
  original_reference_id: PMID:10840044
  qualifier: enables
  review:
    summary: >-
      Direct crystallographic/spectroscopic evidence for NAD+/NADH binding within distinct enzyme
      conformations. A molecular detail underpinning the catalytic mechanism; complementary to the
      core dehydrogenase activity.
    action: KEEP_AS_NON_CORE
    reason: >-
      Cofactor-binding activity supporting, but subordinate to, the core catalytic function.
    supported_by:
    - reference_id: PMID:10840044
      supporting_text: "significant shifting of the NAD(+)-binding domain relative to the C-terminal domain occurs in the ternary and substrate-bound complexes"
- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IDA
  original_reference_id: PMID:10231530
  qualifier: enables
  review:
    summary: >-
      Reflects the fact that HADH is an obligate homodimer, established by crystallography and
      biochemistry. This is a quaternary-structure descriptor ('identical protein binding') rather
      than the bare uninformative 'protein binding', and it is experimentally grounded. It is not,
      however, a core catalytic/regulatory function in its own right.
    action: KEEP_AS_NON_CORE
    reason: >-
      Experimentally supported self-association (homodimerization); structural property rather than
      a core function.
    supported_by:
    - reference_id: PMID:10231530
      supporting_text: "The homodimeric enzyme has been overexpressed in Escherichia coli, purified to homogeneity"
- term:
    id: GO:0003857
    label: (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
  evidence_type: IDA
  original_reference_id: PMID:11489939
  qualifier: enables
  review:
    summary: >-
      Direct assay of the core activity in patient material and recombinant enzyme: SCHAD activity
      was markedly reduced in patient fibroblast mitochondria and the P258L variant had no
      catalytic activity, confirming HADH as the enzyme catalyzing this reaction.
    action: ACCEPT
    reason: >-
      Experimental loss-of-function evidence directly tying HADH to the 3-hydroxyacyl-CoA
      dehydrogenase activity.
    supported_by:
    - reference_id: PMID:11489939
      supporting_text: "Expression studies showed that the P258L enzyme had no catalytic activity"
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: IDA
  original_reference_id: PMID:11489939
  qualifier: involved_in
  review:
    summary: >-
      Direct evidence linking HADH to beta-oxidation: deficiency produces a fatty-acid-oxidation
      disorder with characteristic 3-hydroxy-acylcarnitine accumulation, the first FAO defect
      associated with hyperinsulinism.
    action: ACCEPT
    reason: >-
      Experimentally supported core biological process (beta-oxidation).
    supported_by:
    - reference_id: PMID:11489939
      supporting_text: "This is the first defect in fatty acid beta-oxidation that has been associated with hyperinsulinism"
- term:
    id: GO:0120162
    label: positive regulation of cold-induced thermogenesis
  evidence_type: ISS
  original_reference_id: PMID:21990309
  qualifier: involved_in
  review:
    summary: >-
      Sequence-similarity annotation citing the mouse Hadh knockout thermogenesis phenotype.
      Downstream physiological consequence of impaired fatty-acid oxidation rather than a distinct
      molecular function; retain as non-core.
    action: KEEP_AS_NON_CORE
    reason: >-
      Mouse-derived organismal phenotype downstream of FAO; non-core.
    supported_by:
    - reference_id: PMID:21990309
      supporting_text: "SCHAD plays an important role in adaptive thermogenesis"
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77254
  qualifier: located_in
  review:
    summary: >-
      Reactome traceable assertion placing HADH in the mitochondrial matrix as part of a
      beta-oxidation reaction (3-hydroxydodecanoyl-CoA oxidation). Correct, specific localization
      consistent with UniProt.
    action: ACCEPT
    reason: >-
      Correct, specific mitochondrial matrix localization from curated pathway data.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77312
  qualifier: located_in
  review:
    summary: >-
      Reactome matrix localization within the short-chain (3-hydroxybutanoyl-CoA) beta-oxidation
      reaction. Correct and consistent with the curated location.
    action: ACCEPT
    reason: >-
      Correct mitochondrial matrix localization from curated pathway data.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77323
  qualifier: located_in
  review:
    summary: >-
      Reactome matrix localization within the hexanoyl-CoA beta-oxidation reaction. Correct,
      consistent with curated location.
    action: ACCEPT
    reason: >-
      Correct mitochondrial matrix localization from curated pathway data.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77331
  qualifier: located_in
  review:
    summary: >-
      Reactome matrix localization within the octanoyl-CoA beta-oxidation reaction. Correct,
      consistent with curated location.
    action: ACCEPT
    reason: >-
      Correct mitochondrial matrix localization from curated pathway data.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77342
  qualifier: located_in
  review:
    summary: >-
      Reactome matrix localization within the decanoyl-CoA beta-oxidation reaction. Correct,
      consistent with curated location.
    action: ACCEPT
    reason: >-
      Correct mitochondrial matrix localization from curated pathway data.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9838035
  qualifier: located_in
  review:
    summary: >-
      This Reactome reaction is 'CLPXP binds mitochondrial matrix proteins'; HADH is annotated
      here as a matrix substrate of the quality-control protease, which correctly localizes it to
      the matrix. The location assertion is valid; it does not imply any protease/degradation
      function for HADH itself.
    action: ACCEPT
    reason: >-
      Valid matrix localization arising from HADH being a CLPXP substrate (localization-only, not a
      HADH function).
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9838081
  qualifier: located_in
  review:
    summary: >-
      Reactome 'LONP1 degrades mitochondrial matrix proteins'; HADH appears as a matrix substrate,
      correctly localizing it to the matrix. Location-only evidence, not a degradation function of
      HADH.
    action: ACCEPT
    reason: >-
      Valid matrix localization from HADH being a LONP1 substrate (localization-only).
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9838093
  qualifier: located_in
  review:
    summary: >-
      Reactome 'LONP1 binds mitochondrial matrix proteins'; HADH appears as a matrix substrate.
      Correct localization; location-only, not a HADH function.
    action: ACCEPT
    reason: >-
      Valid matrix localization from HADH being a LONP1 substrate (localization-only).
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9838289
  qualifier: located_in
  review:
    summary: >-
      Reactome 'CLPXP degrades mitochondrial matrix proteins'; HADH appears as a matrix substrate.
      Correct localization; location-only, not a HADH function.
    action: ACCEPT
    reason: >-
      Valid matrix localization from HADH being a CLPXP substrate (localization-only).
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: GO_REF:0000054
  qualifier: located_in
  review:
    summary: >-
      A LIFEdb annotation based on localization of an expressed fluorescent fusion protein in
      living cells. HADH is a mitochondrial matrix enzyme with a cleavable N-terminal mitochondrial
      targeting peptide; a cytoplasmic call most likely reflects mislocalization of the
      overexpressed fusion construct (e.g., incomplete import or a tag obscuring the transit
      peptide) rather than the native location. Contradicted by curated UniProt localization,
      Reactome, HPA, and high-confidence mitochondrial proteomics.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Likely overexpression/fusion-protein artifact; HADH is matrix-localized, not cytoplasmic.
- term:
    id: GO:0003857
    label: (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
  evidence_type: TAS
  original_reference_id: PMID:8687463
  qualifier: enables
  review:
    summary: >-
      Traceable assertion from the original human SCHAD cDNA cloning/characterization paper, which
      identified the protein as short-chain L-3-hydroxyacyl-CoA dehydrogenase. Correct core
      molecular function.
    action: ACCEPT
    reason: >-
      Consistent with the experimentally established core dehydrogenase activity.
    supported_by:
    - reference_id: PMID:8687463
      supporting_text: "The cDNA encompassing the complete coding sequence of human liver short-chain L-3-hydroxyacyl-CoA dehydrogenase (SCHAD) was isolated and characterized"
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: TAS
  original_reference_id: PMID:8687463
  qualifier: located_in
  review:
    summary: >-
      Traceable assertion of mitochondrial localization from the cloning paper, which identified a
      12-residue mitochondrial import signal peptide. Correct; generic relative to the matrix term.
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct mitochondrial localization, less specific than mitochondrial matrix.
    supported_by:
    - reference_id: PMID:8687463
      supporting_text: "containing a mitochondrial import signal peptide of 12 amino acids"
core_functions:
- description: >-
    Core enzymatic function: HADH catalyzes the third step of the mitochondrial fatty-acid
    beta-oxidation spiral, the NAD+-dependent oxidation of L-(3S)-3-hydroxyacyl-CoA to
    3-ketoacyl-CoA, acting as a soluble homodimer in the mitochondrial matrix and preferring
    short/medium-chain (C4-C10) substrates.
  molecular_function:
    id: GO:0003857
    label: (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
  directly_involved_in:
  - id: GO:0006635
    label: fatty acid beta-oxidation
  locations:
  - id: GO:0005759
    label: mitochondrial matrix
  supported_by:
  - reference_id: PMID:10231530
    supporting_text: "catalyzes the oxidation of the hydroxyl group of L-3-hydroxyacyl-CoA to a keto group, concomitant with the reduction of NAD+ to NADH"
  - reference_id: PMID:11489939
    supporting_text: "Expression studies showed that the P258L enzyme had no catalytic activity"
- description: >-
    Secondary (moonlighting) regulatory function: in pancreatic beta-cells HADH binds and
    inhibits the activation of glutamate dehydrogenase 1 (GLUD1), thereby restraining
    amino-acid-stimulated insulin secretion. Loss of HADH de-represses GLUD1 and causes
    inappropriate insulin oversecretion (hyperinsulinaemic hypoglycaemia), a phenotype
    reproduced in Hadh knockout mice and partly independent of beta-oxidation flux. The
    underlying molecular activity is enzyme (GLUD1) inhibitor activity; the physiological
    output is negative regulation of insulin secretion.
  molecular_function:
    id: GO:0004857
    label: enzyme inhibitor activity
  directly_involved_in:
  - id: GO:0046676
    label: negative regulation of insulin secretion
  locations:
  - id: GO:0005759
    label: mitochondrial matrix
  supported_by:
  - reference_id: PMID:20670938
    supporting_text: "showed protein-protein interactions between SCHAD and GDH"
  - reference_id: PMID:20670938
    supporting_text: "reflecting the loss of an inhibitory protein-protein interaction of SCHAD upon GDH"
  - reference_id: PMID:21990309
    supporting_text: "insulin secretion in response to glucose and glucose plus palmitate was elevated in isolated islets of knockout mice"
proposed_new_terms: []
suggested_questions:
- question: >-
    To what extent is HADH's regulation of insulin secretion mediated by direct GLUD1 inhibition
    versus by perturbation of short-chain acyl-CoA/3-hydroxyacyl-CoA pools from impaired
    beta-oxidation, and are these mechanisms separable in human beta-cells?
- question: >-
    Is the HADH-GLUD1 inhibitory interaction conserved and direct in human tissue (as opposed to
    the By-similarity/mouse-based evidence currently underpinning it), and what is its
    stoichiometry and regulation?
suggested_experiments:
- description: >-
    Reconstitute purified human HADH with human GLUD1 in vitro and measure GLUD1 activity +/-
    HADH (and +/- HADH catalytic-dead mutants) to determine whether enzyme-inhibitor activity is
    independent of HADH's own catalysis.
- description: >-
    Generate beta-cell models expressing a catalytically dead but folding-competent HADH variant
    versus full knockout to dissociate the dehydrogenase activity from the GLUD1-inhibition /
    insulin-secretion-restraint function.
- description: >-
    Perform substrate-profiling (chain-length kinetics) on purified human HADH across C4-C16
    3-hydroxyacyl-CoAs to quantitatively confirm short/medium-chain preference and the negligible
    long-chain activity relative to HADHA.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
    by curator judgment of sequence similarity
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- 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: []
- id: GO_REF:0000052
  title: Gene Ontology annotation based on curation of immunofluorescence data
  findings: []
- id: GO_REF:0000054
  title: Gene Ontology annotation based on curation of intracellular localizations
    of expressed fusion proteins in living cells
  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:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:10231530
  title: Biochemical characterization and crystal structure determination of human
    heart short chain L-3-hydroxyacyl-CoA dehydrogenase provide insights into catalytic
    mechanism.
  findings:
  - statement: >-
      Human heart SCHAD catalyzes NAD+-dependent oxidation of L-3-hydroxyacyl-CoA to a 3-keto
      product as part of beta-oxidation; the enzyme is a homodimer and was characterized
      biochemically and crystallographically with NAD+/substrate.
    supporting_text: "catalyzes the oxidation of the hydroxyl group of L-3-hydroxyacyl-CoA to a keto group, concomitant with the reduction of NAD+ to NADH"
  - statement: >-
      Catalytic mechanism: His158 acts as a general base abstracting the 3-OH proton, assisted by
      Glu170.
    supporting_text: "His 158 serves as a general base, abstracting a proton from the 3-OH group of the substrate"
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified primary biochemistry/structure paper establishing the human SCHAD core
      catalytic activity, homodimer, and mechanism. Abstract-only in cache.
- id: PMID:10840044
  title: Sequestration of the active site by interdomain shifting. Crystallographic
    and spectroscopic evidence for distinct conformations of L-3-hydroxyacyl-CoA dehydrogenase.
  findings:
  - statement: >-
      Crystal structures of apo-, cofactor-, and substrate-bound forms reveal NAD+-binding domain
      shifting relative to the C-terminal domain; supports NAD+ binding and catalytic mechanism.
    supporting_text: "significant shifting of the NAD(+)-binding domain relative to the C-terminal domain occurs in the ternary and substrate-bound complexes"
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified structural follow-up supporting NAD+ binding and the catalytic conformational
      cycle. Abstract-only in cache.
- id: PMID:11489939
  title: Hyperinsulinism in short-chain L-3-hydroxyacyl-CoA dehydrogenase deficiency
    reveals the importance of beta-oxidation in insulin secretion.
  findings:
  - statement: >-
      First report linking a fatty-acid-oxidation defect (SCHAD/HADH deficiency, P258L) to
      hyperinsulinism, establishing HADH's role in insulin-secretion regulation.
    supporting_text: "This is the first defect in fatty acid beta-oxidation that has been associated with hyperinsulinism"
  - statement: >-
      The disease-causing P258L variant abolishes catalytic activity, directly tying HADH to the
      3-hydroxyacyl-CoA dehydrogenase reaction.
    supporting_text: "Expression studies showed that the P258L enzyme had no catalytic activity"
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified case report establishing the HADH-hyperinsulinism link and confirming loss of
      catalytic activity in a pathogenic variant. Abstract-only in cache.
- id: PMID:16725361
  title: Reye-like syndrome resulting from novel missense mutations in mitochondrial
    medium- and short-chain l-3-hydroxy-acyl-CoA dehydrogenase.
  findings:
  - statement: >-
      Kinetic analysis of patient-derived M/SCHAD mutants (D45G altered NADH Km; Y214H no activity)
      confirms the human enzyme's 3-hydroxyacyl-CoA dehydrogenase activity and broadens the
      phenotype; supports a role in insulin regulation.
    supporting_text: "This association suggests that there is a role for M/SCHAD in regulating the pancreatic secretion of insulin"
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified case report with mutant enzymology supporting the core activity and the
      insulin-regulation role. Abstract-only in cache.
- id: PMID:20670938
  title: Mechanism of hyperinsulinism in short-chain 3-hydroxyacyl-CoA dehydrogenase
    deficiency involves activation of glutamate dehydrogenase.
  findings:
  - statement: >-
      Definitive mechanistic paper: pull-down experiments demonstrate a direct protein-protein
      interaction between SCHAD (HADH) and glutamate dehydrogenase (GDH), and show that SCHAD
      deficiency activates GDH by removing this inhibitory interaction, dysregulating
      amino-acid-stimulated insulin secretion. Establishes the GLUD1-inhibitor moonlighting
      function on firmer footing than the earlier speculative reports.
    supporting_text: "reflecting the loss of an inhibitory protein-protein interaction of SCHAD upon GDH"
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified, full text available; provides the definitive protein-protein interaction and
      loss-of-inhibition evidence for the HADH/GLUD1 regulatory function.
- id: PMID:21990309
  title: Role of medium- and short-chain L-3-hydroxyacyl-CoA dehydrogenase in the
    regulation of body weight and thermogenesis.
  findings:
  - statement: >-
      Hadh-knockout mice show low glucose and elevated insulin, and isolated islets hypersecrete
      insulin in response to glucose and palmitate, supporting HADH's negative regulation of
      insulin secretion.
    supporting_text: "insulin secretion in response to glucose and glucose plus palmitate was elevated in isolated islets of knockout mice"
  - statement: >-
      Hadh knockout impairs adaptive thermogenesis and body-weight regulation under high-fat/cold
      conditions.
    supporting_text: "SCHAD plays an important role in adaptive thermogenesis"
  - statement: >-
      SCHAD/HADH is highly expressed in pancreatic islets of Langerhans, consistent with a direct
      role in beta-cell function.
    supporting_text: "in the islets of Langerhans within the pancreas"
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified mouse knockout study (full text available) supporting insulin-secretion
      regulation, thermogenesis, and islet expression.
- id: PMID:34800366
  title: Quantitative high-confidence human mitochondrial proteome and its dynamics
    in cellular context.
  findings:
  - statement: >-
      HADH is identified in a high-confidence quantitative human mitochondrial proteome,
      corroborating its mitochondrial localization.
    supporting_text: "Quantitative high-confidence human mitochondrial proteome and its dynamics"
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      High-throughput mitochondrial proteomics providing orthogonal support for mitochondrial
      localization.
- id: PMID:8687463
  title: 'Human short-chain L-3-hydroxyacyl-CoA dehydrogenase: cloning and characterization
    of the coding sequence.'
  findings:
  - statement: >-
      Original cloning of human SCHAD cDNA; encodes a 314-aa protein with a 12-residue
      mitochondrial import peptide; expressed in liver, kidney, pancreas, heart and skeletal
      muscle.
    supporting_text: "Northern blot analysis reveals SCHAD mRNA to be expressed in liver, kidney, pancreas, heart and skeletal muscle"
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified original characterization establishing identity, mitochondrial targeting, and
      tissue expression. Abstract-only in cache.
- id: Reactome:R-HSA-77254
  title: (S)-3-Hydroxydodecanoyl-CoA+NAD => 3-Oxododecanoyl-CoA+NADH+H
  findings: []
- id: Reactome:R-HSA-77312
  title: (S)-Hydroxybutanoyl-CoA+NAD => Acetoacetyl-CoA+NADH+H
  findings: []
- id: Reactome:R-HSA-77323
  title: (S)-Hydroxyhexanoyl-CoA+NAD => 3-Oxohexanoyl-CoA+NADH+H
  findings: []
- id: Reactome:R-HSA-77331
  title: (S)-Hydroxyoctanoyl-CoA+NAD => 3-Oxooctanoyl-CoA+NADH+H
  findings: []
- id: Reactome:R-HSA-77342
  title: (S)-Hydroxydecanoyl-CoA+NAD => 3-Oxodecanoyl-CoA+NADH+H
  findings: []
- id: Reactome:R-HSA-9838035
  title: CLPXP binds mitochondrial matrix proteins
  findings: []
- id: Reactome:R-HSA-9838081
  title: LONP1 degrades mitochondrial matrix proteins
  findings: []
- id: Reactome:R-HSA-9838093
  title: LONP1 binds mitochondrial matrix proteins
  findings: []
- id: Reactome:R-HSA-9838289
  title: CLPXP degrades mitochondrial matrix proteins
  findings: []