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.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003857 (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity | IBA GO_REF:0000033 | ACCEPT | 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. 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). Supporting Evidence: PMID:10231530 catalyzes the oxidation of the hydroxyl group of L-3-hydroxyacyl-CoA to a keto group, concomitant with the reduction of NAD+ to NADH |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | KEEP AS NON CORE | 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. Reason: Correct compartment but less specific than the supported mitochondrial matrix annotation. |
| GO:0006635 fatty acid beta-oxidation | IBA GO_REF:0000033 | ACCEPT | 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. Reason: Directly supported by experimental data and UniProt pathway curation (lipid metabolism; fatty acid beta-oxidation). Supporting Evidence: PMID:11489939 This is the first defect in fatty acid beta-oxidation that has been associated with hyperinsulinism |
| GO:0003857 (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic (multi-method) inference of the core catalytic activity. Redundant with the experimental and IBA annotations on the same term and correct. Reason: Same correct molecular function as the experimentally supported annotation. |
| GO:0005759 mitochondrial matrix | IEA GO_REF:0000044 | ACCEPT | 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. Reason: Matches the curated UniProt 'Mitochondrion matrix' location and is the most precise localization for HADH. |
| GO:0006631 fatty acid metabolic process | IEA GO_REF:0000002 | KEEP AS NON CORE | 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. Reason: Subsumed by the more specific beta-oxidation annotation. |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000002 | KEEP AS NON CORE | 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. Reason: Generic parent of the specific dehydrogenase activity; uninformative as a standalone core function. |
| GO:0016509 long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity | IEA GO_REF:0000116 | MARK AS OVER ANNOTATED | 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. 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. |
| GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | IEA GO_REF:0000002 | KEEP AS NON CORE | 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. Reason: Generic parent of the specific 3-hydroxyacyl-CoA dehydrogenase activity. |
| GO:0070403 NAD+ binding | IEA GO_REF:0000002 | KEEP AS NON CORE | 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. Reason: Cofactor-binding activity supporting the core catalytic function; also captured by the IDA annotation from PMID:10840044. |
| GO:0005739 mitochondrion | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Correct mitochondrial localization by orthology transfer, but generic relative to the specific 'mitochondrial matrix' term. Reason: Less specific than the supported mitochondrial matrix annotation. |
| GO:0006635 fatty acid beta-oxidation | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic inference of the core beta-oxidation process, redundant with and consistent with the experimental (IDA) and IBA annotations on this term. Reason: Correct core biological process supported by experimental evidence. |
| GO:0009410 response to xenobiotic stimulus | IEA GO_REF:0000107 | KEEP AS NON CORE | 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. Reason: Orthology-transferred generic response term; not contradicted but low information and not a core function. |
| GO:0009725 response to hormone | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Generic 'response to hormone' transferred electronically from a rodent ortholog. Broad and mechanistically uninformative for HADH. Reason: Orthology-transferred generic term; non-core. |
| GO:0014823 response to activity | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Generic physiological response term transferred from a rodent ortholog; not informative about HADH molecular function. Reason: Orthology-transferred generic term; non-core. |
| GO:0032868 response to insulin | IEA GO_REF:0000107 | KEEP AS NON CORE | 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. Reason: Orthology-transferred generic response term; the relevant insulin biology is captured by the regulation-of-insulin-secretion annotations. |
| GO:0046676 negative regulation of insulin secretion | IEA GO_REF:0000107 | KEEP AS NON CORE | 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. Reason: Well-supported regulatory function (GDH inhibition / restraint of insulin secretion), but secondary to the core beta-oxidation enzymatic role. Supporting Evidence: PMID:21990309 insulin secretion in response to glucose and glucose plus palmitate was elevated in isolated islets of knockout mice |
| GO:0050796 regulation of insulin secretion | IEA GO_REF:0000107 | KEEP AS NON CORE | 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. Reason: Correct regulatory role but subsumed by the more specific negative-regulation term. |
| GO:0120162 positive regulation of cold-induced thermogenesis | IEA GO_REF:0000107 | KEEP AS NON CORE | 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. Reason: Mouse-derived physiological phenotype downstream of FAO; non-core. Supporting Evidence: PMID:21990309 SCHAD plays an important role in adaptive thermogenesis |
| GO:0005739 mitochondrion | IDA GO_REF:0000052 | KEEP AS NON CORE | Summary: Direct (immunofluorescence/HPA) evidence for mitochondrial localization. Correct; generic relative to the matrix sub-compartment but a valid experimental localization. Reason: Experimentally supported mitochondrial localization, less specific than mitochondrial matrix. |
| GO:0003857 (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity | EXP PMID:10231530 Biochemical characterization and crystal structure determina... | ACCEPT | 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. Reason: Gold-standard experimental evidence for the core dehydrogenase activity. Supporting Evidence: PMID:10231530 catalyzes the oxidation of the hydroxyl group of L-3-hydroxyacyl-CoA to a keto group, concomitant with the reduction of NAD+ to NADH |
| GO:0003857 (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity | EXP PMID:16725361 Reye-like syndrome resulting from novel missense mutations i... | ACCEPT | 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. Reason: Independent experimental confirmation of the core dehydrogenase activity through mutant enzymology. |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | KEEP AS NON CORE | 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. Reason: Supports mitochondrial localization; less specific than mitochondrial matrix. |
| GO:0050796 regulation of insulin secretion | ISS GO_REF:0000024 | KEEP AS NON CORE | 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. Reason: Genuine but secondary regulatory function; the negative-regulation term is more precise. Supporting Evidence: PMID:21990309 Blood glucose concentrations in the fasted and postprandial state were significantly lower in hadh(-/-) mice, whereas insulin levels were elevated |
| GO:0070403 NAD+ binding | IDA PMID:10840044 Sequestration of the active site by interdomain shifting. Cr... | KEEP AS NON CORE | 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. Reason: Cofactor-binding activity supporting, but subordinate to, the core catalytic function. Supporting Evidence: PMID:10840044 significant shifting of the NAD(+)-binding domain relative to the C-terminal domain occurs in the ternary and substrate-bound complexes |
| GO:0042802 identical protein binding | IDA PMID:10231530 Biochemical characterization and crystal structure determina... | KEEP AS NON CORE | 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. Reason: Experimentally supported self-association (homodimerization); structural property rather than a core function. Supporting Evidence: PMID:10231530 The homodimeric enzyme has been overexpressed in Escherichia coli, purified to homogeneity |
| GO:0003857 (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity | IDA PMID:11489939 Hyperinsulinism in short-chain L-3-hydroxyacyl-CoA dehydroge... | ACCEPT | 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. Reason: Experimental loss-of-function evidence directly tying HADH to the 3-hydroxyacyl-CoA dehydrogenase activity. Supporting Evidence: PMID:11489939 Expression studies showed that the P258L enzyme had no catalytic activity |
| GO:0006635 fatty acid beta-oxidation | IDA PMID:11489939 Hyperinsulinism in short-chain L-3-hydroxyacyl-CoA dehydroge... | ACCEPT | 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. Reason: Experimentally supported core biological process (beta-oxidation). Supporting Evidence: PMID:11489939 This is the first defect in fatty acid beta-oxidation that has been associated with hyperinsulinism |
| GO:0120162 positive regulation of cold-induced thermogenesis | ISS PMID:21990309 Role of medium- and short-chain L-3-hydroxyacyl-CoA dehydrog... | KEEP AS NON CORE | 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. Reason: Mouse-derived organismal phenotype downstream of FAO; non-core. Supporting Evidence: PMID:21990309 SCHAD plays an important role in adaptive thermogenesis |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-77254 | ACCEPT | 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. Reason: Correct, specific mitochondrial matrix localization from curated pathway data. |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-77312 | ACCEPT | Summary: Reactome matrix localization within the short-chain (3-hydroxybutanoyl-CoA) beta-oxidation reaction. Correct and consistent with the curated location. Reason: Correct mitochondrial matrix localization from curated pathway data. |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-77323 | ACCEPT | Summary: Reactome matrix localization within the hexanoyl-CoA beta-oxidation reaction. Correct, consistent with curated location. Reason: Correct mitochondrial matrix localization from curated pathway data. |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-77331 | ACCEPT | Summary: Reactome matrix localization within the octanoyl-CoA beta-oxidation reaction. Correct, consistent with curated location. Reason: Correct mitochondrial matrix localization from curated pathway data. |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-77342 | ACCEPT | Summary: Reactome matrix localization within the decanoyl-CoA beta-oxidation reaction. Correct, consistent with curated location. Reason: Correct mitochondrial matrix localization from curated pathway data. |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-9838035 | ACCEPT | 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. Reason: Valid matrix localization arising from HADH being a CLPXP substrate (localization-only, not a HADH function). |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-9838081 | ACCEPT | 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. Reason: Valid matrix localization from HADH being a LONP1 substrate (localization-only). |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-9838093 | ACCEPT | Summary: Reactome 'LONP1 binds mitochondrial matrix proteins'; HADH appears as a matrix substrate. Correct localization; location-only, not a HADH function. Reason: Valid matrix localization from HADH being a LONP1 substrate (localization-only). |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-9838289 | ACCEPT | Summary: Reactome 'CLPXP degrades mitochondrial matrix proteins'; HADH appears as a matrix substrate. Correct localization; location-only, not a HADH function. Reason: Valid matrix localization from HADH being a CLPXP substrate (localization-only). |
| GO:0005737 cytoplasm | IDA GO_REF:0000054 | MARK AS OVER ANNOTATED | 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. Reason: Likely overexpression/fusion-protein artifact; HADH is matrix-localized, not cytoplasmic. |
| GO:0003857 (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity | TAS PMID:8687463 Human short-chain L-3-hydroxyacyl-CoA dehydrogenase: cloning... | ACCEPT | 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. Reason: Consistent with the experimentally established core dehydrogenase activity. Supporting Evidence: PMID:8687463 The cDNA encompassing the complete coding sequence of human liver short-chain L-3-hydroxyacyl-CoA dehydrogenase (SCHAD) was isolated and characterized |
| GO:0005739 mitochondrion | TAS PMID:8687463 Human short-chain L-3-hydroxyacyl-CoA dehydrogenase: cloning... | KEEP AS NON CORE | 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. Reason: Correct mitochondrial localization, less specific than mitochondrial matrix. Supporting Evidence: PMID:8687463 containing a mitochondrial import signal peptide of 12 amino acids |
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Download this section (compressed HTML)Q: 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?
Q: 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?
Experiment: 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.
Experiment: 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.
Experiment: 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.
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