DHTKD1 is the E1 component (E1a; 2-oxoadipate dehydrogenase, OADH-E1) of the mitochondrial 2-oxoadipate dehydrogenase complex (OADHC). It is a thiamine diphosphate (ThDP)-dependent decarboxylase and a paralog of OGDH, the 2-oxoglutarate dehydrogenase E1. DHTKD1 catalyzes the first, rate-limiting and irreversible step of the complex: the oxidative decarboxylation of 2-oxoadipate (alpha-ketoadipate), transferring the decarboxylated glutaryl intermediate onto the lipoyl group of the shared E2 subunit (DLST), with the overall complex producing glutaryl-CoA and CO2. OADHC uses the same E2 (DLST) and E3 (DLD) components as the TCA-cycle 2-oxoglutarate dehydrogenase complex, but the E1 subunit is complex-specific; DHTKD1 strongly prefers 2-oxoadipate over 2-oxoglutarate as substrate. This reaction is the final common step of L-lysine, L-hydroxylysine and L-tryptophan degradation, whose convergent intermediate is 2-oxoadipate. The enzyme functions as a homodimer in the mitochondrial matrix. Loss-of-function variants cause alpha-aminoadipic and alpha-ketoadipic aciduria (AAKAD, frequently benign), and DHTKD1 has also been linked to axonal Charcot-Marie-Tooth disease type 2Q.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005739
mitochondrion
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: Subcellular-location IEA placing DHTKD1 in the mitochondrion, consistent with all experimental evidence and the mitochondrial transit peptide. Correct but less precise than the mitochondrial matrix localization supported by Reactome/Ensembl orthology.
Reason: DHTKD1 is a validated mitochondrial matrix enzyme (UniProt SUBCELLULAR LOCATION, PMID:23141294). The generic mitochondrion term is correct.
Supporting Evidence:
PMID:23141294
implicating an important role for DHTKD1 in mitochondrial energy production and neurological development.
|
|
GO:0016624
oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
|
IEA
GO_REF:0000120 |
MARK AS OVER ANNOTATED |
Summary: Broad InterPro/orthology-based oxidoreductase term describing the overall E1+E2+E3 (disulfide-acceptor) chemistry of the 2-oxo-acid dehydrogenase family. The precise activity of the E1a subunit is the ThDP-dependent decarboxylation captured by GO:0160166.
Reason: This family-level term describes the full dehydrogenase complex reaction in which the ultimate electron acceptor is a disulfide (lipoyl/E3). The DHTKD1 E1a subunit itself performs ThDP-dependent decarboxylation of 2-oxoadipate and transfers the acyl group to the E2 lipoyl moiety; the more specific and accurate MF for DHTKD1 is GO:0160166 (2-oxoadipate dehydrogenase activity), which is separately annotated with IDA support.
Supporting Evidence:
PMID:29191460
It is involved in the oxidative decarboxylation of 2-oxoadipate (OA) to glutaryl-CoA on the final degradative pathway of L-lysine
|
|
GO:0030976
thiamine pyrophosphate binding
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: InterPro-based annotation of thiamine diphosphate (ThDP) binding. ThDP is the essential catalytic cofactor of DHTKD1, confirmed biochemically and by crystal structures of the DHTKD1-ThDP complex.
Reason: DHTKD1 is a ThDP-dependent decarboxylase; ThDP is documented as its cofactor (UniProt COFACTOR, PMID:32695416; DHTKD1-ThDP crystal structure PMID:32633484). The InterPro TPP-binding domain (IPR011603/IPR029061) is present. This is a core molecular function.
Supporting Evidence:
PMID:29191460
Herein are reported unique properties of the novel human thiamin diphosphate (ThDP)-dependent enzyme 2-oxoadipate dehydrogenase (hE1a)
|
|
GO:0160166
2-oxoadipate dehydrogenase activity
|
IEA
GO_REF:0000116 |
ACCEPT |
Summary: RHEA-mapped IEA for the core catalytic activity of DHTKD1: the ThDP-dependent oxidative decarboxylation of 2-oxoadipate (RHEA:69576). This is the primary, experimentally validated molecular function.
Reason: Matches the reaction assigned in UniProt (RHEA:69576) and is directly supported by biochemistry (PMID:29191460, PMID:32633484) and structure. Duplicate of the IDA-supported GO:0160166 below; both are correct.
Supporting Evidence:
PMID:29191460
hE1a displays an approximately 49-fold preference in catalytic efficiency for OA over OG, indicating that hE1a is specific to the 2-oxoadipate dehydrogenase complex
|
|
GO:0005515
protein binding
|
IPI
PMID:28514442 Architecture of the human interactome defines protein commun... |
MARK AS OVER ANNOTATED |
Summary: High-throughput affinity-purification/mass-spectrometry interactome (BioPlex 2.0) IPI to PGLYRP3 (Q96LB9). Bare "protein binding" is uninformative about DHTKD1's molecular function.
Reason: This is a proteome-scale AP-MS screen, not a directed study of DHTKD1's biology; the recorded partner (PGLYRP3) has no established functional relationship to 2-oxoadipate catabolism. Per curation guidance, bare GO:0005515 protein binding IPIs are uninformative and are marked as over-annotation rather than removed. The biologically meaningful interaction of DHTKD1 is with the E2 subunit DLST, captured by the oxoadipate dehydrogenase complex annotation.
Supporting Evidence:
PMID:28514442
BioPlex 2.0 exceeds previous experimentally derived interaction networks in depth and breadth
|
|
GO:0005515
protein binding
|
IPI
PMID:32296183 A reference map of the human binary protein interactome. |
MARK AS OVER ANNOTATED |
Summary: Binary yeast-two-hybrid interactome (HuRI) IPI to an isoform of BMAL1 (O00327-8). Bare "protein binding" is uninformative about DHTKD1's molecular function.
Reason: This is a genome-scale binary interaction map, not a directed functional study of DHTKD1. The reported partner has no established role in 2-oxoadipate/lysine catabolism. Per curation guidance, bare protein binding IPIs are marked as over-annotation rather than removed.
Supporting Evidence:
PMID:32296183
A reference map of the human binary protein interactome.
|
|
GO:0005515
protein binding
|
IPI
PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... |
MARK AS OVER ANNOTATED |
Summary: High-throughput AP-MS interactome (BioPlex-derived, cell-specific networks) IPI to PGLYRP3 (Q96LB9). Bare "protein binding" is uninformative about DHTKD1's molecular function.
Reason: Proteome-scale interactome dataset rather than a directed DHTKD1 study; the reported partner has no established connection to 2-oxoadipate catabolism. Per curation guidance, bare protein binding IPIs are marked as over-annotation rather than removed.
Supporting Evidence:
PMID:33961781
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
|
|
GO:0005759
mitochondrial matrix
|
IEA
GO_REF:0000107 |
ACCEPT |
Summary: Orthology-based (Ensembl Compara) is_active_in annotation to the mitochondrial matrix, transferred from mouse ortholog. Consistent with the matrix localization of a soluble ThDP-dependent dehydrogenase.
Reason: DHTKD1 has an N-terminal mitochondrial transit peptide and functions as a soluble matrix enzyme of the OADHC; matrix localization is supported by Reactome and by the shared architecture with the OGDH complex.
Supporting Evidence:
PMID:29191460
the dihydrolipoyl succinyltransferase (hE2o) and the dihydrolipoyl dehydrogenase (hE3) components of the tricarboxylic acid cycle 2-oxoglutarate dehydrogenase complex (OGDHc) for its activity
|
|
GO:0009063
amino acid catabolic process
|
IEA
GO_REF:0000107 |
KEEP AS NON CORE |
Summary: Orthology-based involvement in amino acid catabolism. Correct but a generic parent of the specific L-lysine/L-tryptophan catabolic processes DHTKD1 participates in.
Reason: Accurate at a high level (DHTKD1 acts on the convergent 2-oxoadipate step of lysine/hydroxylysine/tryptophan degradation) but subsumed by the more specific L-lysine catabolic process (GO:0019477). Retained as non-core background rather than as a distinct core function.
Supporting Evidence:
PMID:29191460
on the final degradative pathway of L-lysine and is critical for mitochondrial metabolism
|
|
GO:0019477
L-lysine catabolic process
|
IEA
GO_REF:0000107 |
ACCEPT |
Summary: Orthology-based annotation to L-lysine catabolism. This is the principal biological process in which DHTKD1 acts, catalyzing the final common 2-oxoadipate step of the lysine (and hydroxylysine/tryptophan) degradation pathway.
Reason: Well supported: DHTKD1 performs the rate-limiting decarboxylation of 2-oxoadipate, the convergent intermediate of L-lysine catabolism; disease variants cause elevated 2-oxoadipate/2-aminoadipate. Core process.
Supporting Evidence:
PMID:29191460
It is involved in the oxidative decarboxylation of 2-oxoadipate (OA) to glutaryl-CoA on the final degradative pathway of L-lysine
|
|
GO:0005739
mitochondrion
|
IDA
GO_REF:0000052 |
ACCEPT |
Summary: Immunofluorescence-based (HPA) IDA localizing DHTKD1 to the mitochondrion. Consistent with all other evidence.
Reason: Directly observed mitochondrial localization by immunofluorescence, concordant with the mitochondrial matrix function of the OADHC E1a subunit.
Supporting Evidence:
PMID:23141294
implicating an important role for DHTKD1 in mitochondrial energy production and neurological development.
|
|
GO:0005739
mitochondrion
|
HTP
PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... |
ACCEPT |
Summary: High-throughput mitochondrial proteomics (MitoCoP) detecting DHTKD1 in the high-confidence human mitochondrial proteome.
Reason: Independent proteomic confirmation of mitochondrial localization, consistent with the transit peptide and matrix function.
Supporting Evidence:
PMID:34800366
defined a mitochondrial high-confidence proteome of >1,100 proteins (MitoCoP)
|
|
GO:0160166
2-oxoadipate dehydrogenase activity
|
IDA
PMID:29191460 The mitochondrial 2-oxoadipate and 2-oxoglutarate dehydrogen... |
ACCEPT |
Summary: Direct biochemical demonstration that recombinant human E1a (DHTKD1) oxidatively decarboxylates 2-oxoadipate, with ~49-fold catalytic preference for 2-oxoadipate over 2-oxoglutarate. This is the defining, experimentally validated molecular function of the gene.
Reason: Gold-standard IDA evidence for the core catalytic activity; corroborated by kinetics (KM 0.012-0.015 mM for 2-oxoadipate) and crystal structures (PMID:32633484, PMID:32695416).
Supporting Evidence:
PMID:29191460
hE1a displays an approximately 49-fold preference in catalytic efficiency for OA over OG, indicating that hE1a is specific to the 2-oxoadipate dehydrogenase complex
|
|
GO:0160167
oxoadipate dehydrogenase complex
|
IDA
PMID:29191460 The mitochondrial 2-oxoadipate and 2-oxoglutarate dehydrogen... |
ACCEPT |
Summary: DHTKD1 is the E1a subunit of the 2-oxoadipate dehydrogenase complex, which it forms together with the shared E2 (DLST) and E3 (DLD) components of the 2-oxoglutarate dehydrogenase machinery. Directly demonstrated by reconstitution of an active complex.
Reason: Core cellular-component annotation. DHTKD1 recruits E2 (DLST) and E3 (DLD) to assemble a functional OADHC; the E1 subunit is complex-specific. This is the biologically meaningful protein-protein assembly for DHTKD1.
Supporting Evidence:
PMID:29191460
The hE1a has recruited the dihydrolipoyl succinyltransferase (hE2o) and the dihydrolipoyl dehydrogenase (hE3) components of the tricarboxylic acid cycle 2-oxoglutarate dehydrogenase complex (OGDHc) for its activity
|
|
GO:0005759
mitochondrial matrix
|
TAS
Reactome:R-HSA-9858321 |
ACCEPT |
Summary: Reactome TAS localizing the DHTKD1-catalyzed 2-oxoadipate decarboxylation to the mitochondrial matrix, the compartment of the OADHC.
Reason: Consistent with the soluble matrix location of the E1a subunit of the OADHC and with orthology/proteomic evidence.
Supporting Evidence:
PMID:29191460
the tricarboxylic acid cycle 2-oxoglutarate dehydrogenase complex (OGDHc) for its activity
|
|
GO:0005759
mitochondrial matrix
|
TAS
Reactome:R-HSA-9858589 |
ACCEPT |
Summary: Reactome TAS localizing the OADHC E3 (DLD) dihydrolipoyl dehydrogenation step to the mitochondrial matrix, the compartment where DHTKD1 acts.
Reason: Matrix localization is well established for the OADHC in which DHTKD1 is the E1 subunit.
Supporting Evidence:
PMID:29191460
the dihydrolipoyl dehydrogenase (hE3) components of the tricarboxylic acid cycle 2-oxoglutarate dehydrogenase complex (OGDHc) for its activity
|
|
GO:0005759
mitochondrial matrix
|
TAS
Reactome:R-HSA-9858590 |
ACCEPT |
Summary: Reactome TAS localizing the OADHC E2 (DLST) glutaryl transfer to CoA in the mitochondrial matrix, the compartment where DHTKD1 acts.
Reason: Consistent with matrix localization of the OADHC and of DHTKD1.
Supporting Evidence:
PMID:29191460
the dihydrolipoyl succinyltransferase (hE2o) and the dihydrolipoyl dehydrogenase (hE3) components of the tricarboxylic acid cycle 2-oxoglutarate dehydrogenase complex (OGDHc) for its activity
|
|
GO:0005739
mitochondrion
|
IDA
PMID:23141294 A nonsense mutation in DHTKD1 causes Charcot-Marie-Tooth dis... |
ACCEPT |
Summary: IDA localizing DHTKD1 to the mitochondrion, from the study that established the DHTKD1-CMT2 link and reported subcellular localization.
Reason: Direct experimental evidence for mitochondrial localization (UniProt SUBCELLULAR LOCATION cites this paper); concordant with all other data.
Supporting Evidence:
PMID:23141294
implicating an important role for DHTKD1 in mitochondrial energy production and neurological development.
|
|
GO:0006091
generation of precursor metabolites and energy
|
IMP
PMID:23141294 A nonsense mutation in DHTKD1 causes Charcot-Marie-Tooth dis... |
MARK AS OVER ANNOTATED |
Summary: IMP from a DHTKD1-silencing study reporting decreased ATP and total NAD(+)/NADH. This is a downstream physiological consequence of losing a lysine-catabolic enzyme rather than a direct biological process of DHTKD1.
Reason: DHTKD1 knockdown reduces cellular ATP/NAD(H) (an indirect metabolic readout), but DHTKD1 is not part of primary energy-generating machinery such as the TCA cycle or oxidative phosphorylation; its direct role is the 2-oxoadipate step of amino-acid (lysine/tryptophan) catabolism. This term over-generalizes a secondary phenotype. Note this contrasts with the OGDH paralog, which is a bona fide TCA-cycle energy enzyme. Retained (not removed) as it derives from an experimental IMP.
Supporting Evidence:
PMID:23141294
DHTKD1 silencing was found to lead to impaired energy production, evidenced by decreased ATP, total NAD(+) and NADH, and NADH levels
|
|
GO:0006569
L-tryptophan catabolic process
|
IEA
PMID:29191460 The mitochondrial 2-oxoadipate and 2-oxoglutarate dehydrogen... |
NEW |
Summary: Proposed additional biological-process annotation. 2-oxoadipate is the convergent intermediate of L-lysine, L-hydroxylysine AND L-tryptophan catabolism; by decarboxylating 2-oxoadipate, DHTKD1 catalyzes the final common step of the tryptophan degradation pathway as well as the lysine pathway.
Reason: UniProt explicitly states DHTKD1 is responsible for the last step of L-lysine, L-hydroxylysine and L-tryptophan catabolism (common product 2-oxoadipate). The tryptophan-catabolic role is not otherwise captured in GOA and complements the existing L-lysine catabolic process annotation.
Supporting Evidence:
PMID:29191460
It is involved in the oxidative decarboxylation of 2-oxoadipate (OA) to glutaryl-CoA on the final degradative pathway of L-lysine
|
Q: Given that DHTKD1 shares E2 (DLST) and E3 (DLD) with the 2-oxoglutarate dehydrogenase complex, how is flux partitioned between the OGDHC and OADHC in tissues where both are expressed (e.g. liver)?
Q: Why is alpha-aminoadipic/alpha-ketoadipic aciduria caused by DHTKD1 loss so frequently asymptomatic, and what genetic or metabolic factors modify the CMT2Q neuropathy phenotype?
Experiment: Tissue-resolved metabolic flux analysis (e.g. 13C-lysine tracing) in DHTKD1-knockout versus wild-type cells to quantify the contribution of DHTKD1 to 2-oxoadipate turnover and downstream glutaryl-CoA and energy metabolism.
Hypothesis: DHTKD1 loss diverts 2-oxoadipate away from glutaryl-CoA, causing measurable accumulation of 2-oxoadipate/2-aminoadipate without major bioenergetic deficit.
Experiment: Structural and kinetic characterization of the assembled DHTKD1-DLST-DLD megacomplex to define substrate channeling and the effect of AAKAD variants (e.g. G729R, R715C) on complex assembly and activity.
Hypothesis: AAKAD-causing variants impair DHTKD1-DLST assembly, disrupting intermediate channeling rather than abolishing intrinsic decarboxylase chemistry.
just deep-research-falcon human Q96HY7 --alias DHTKD1 failed in this environment:
scripts/deep_research_wrapper.py uses X | None type-union syntax that raises
TypeError: unsupported operand type(s) for | under the interpreter available here
(recipe fails on line 218). The OLS MCP also errored (No module named 'rich.traceback').
No -deep-research-*.md file was fabricated. Review is grounded in the UniProt record
(DHTKD1-uniprot.txt), the seeded GOA, and cached publications/PMID_*.md. GO term
labels/aspects/obsolescence were verified directly against the QuickGO REST API.
GO:0160166 2-oxoadipate dehydrogenase activity — IDA (PMID:29191460) + RHEA IEA:GO:0016624 (oxidoreductase, aldehyde/oxo donor, disulfide acceptor) IEA: parent ofGO:0030976 thiamine pyrophosphate binding IEA: ACCEPT — ThDP is the cofactorGO:0005515 protein binding IPIs are from high-throughput interactomemitochondrion calls are correct but less precise than mitochondrial matrix.GO:0160167 oxoadipate dehydrogenase complex IDA (PMID:29191460): ACCEPT — core.GO:0019477 L-lysine catabolic process IEA: ACCEPT (core pathway).GO:0009063 amino acid catabolic process IEA: correct but generic parent →GO:0006091 generation of precursor metabolites and energy IMP (PMID:23141294):id: Q96HY7
gene_symbol: DHTKD1
product_type: PROTEIN
status: INITIALIZED
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
DHTKD1 is the E1 component (E1a; 2-oxoadipate dehydrogenase, OADH-E1) of the
mitochondrial 2-oxoadipate dehydrogenase complex (OADHC). It is a thiamine
diphosphate (ThDP)-dependent decarboxylase and a paralog of OGDH, the
2-oxoglutarate dehydrogenase E1. DHTKD1 catalyzes the first, rate-limiting and
irreversible step of the complex: the oxidative decarboxylation of 2-oxoadipate
(alpha-ketoadipate), transferring the decarboxylated glutaryl intermediate onto
the lipoyl group of the shared E2 subunit (DLST), with the overall complex
producing glutaryl-CoA and CO2. OADHC uses the same E2 (DLST) and E3 (DLD)
components as the TCA-cycle 2-oxoglutarate dehydrogenase complex, but the E1
subunit is complex-specific; DHTKD1 strongly prefers 2-oxoadipate over
2-oxoglutarate as substrate. This reaction is the final common step of L-lysine,
L-hydroxylysine and L-tryptophan degradation, whose convergent intermediate is
2-oxoadipate. The enzyme functions as a homodimer in the mitochondrial matrix.
Loss-of-function variants cause alpha-aminoadipic and alpha-ketoadipic aciduria
(AAKAD, frequently benign), and DHTKD1 has also been linked to axonal
Charcot-Marie-Tooth disease type 2Q.
existing_annotations:
- term:
id: GO:0005739
label: mitochondrion
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: >-
Subcellular-location IEA placing DHTKD1 in the mitochondrion, consistent
with all experimental evidence and the mitochondrial transit peptide.
Correct but less precise than the mitochondrial matrix localization
supported by Reactome/Ensembl orthology.
action: ACCEPT
reason: >-
DHTKD1 is a validated mitochondrial matrix enzyme (UniProt SUBCELLULAR
LOCATION, PMID:23141294). The generic mitochondrion term is correct.
supported_by:
- reference_id: PMID:23141294
supporting_text: >-
implicating an important role for DHTKD1 in mitochondrial energy
production and neurological development.
- term:
id: GO:0016624
label: oxidoreductase activity, acting on the aldehyde or oxo group of donors,
disulfide as acceptor
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: >-
Broad InterPro/orthology-based oxidoreductase term describing the
overall E1+E2+E3 (disulfide-acceptor) chemistry of the 2-oxo-acid
dehydrogenase family. The precise activity of the E1a subunit is the
ThDP-dependent decarboxylation captured by GO:0160166.
action: MARK_AS_OVER_ANNOTATED
reason: >-
This family-level term describes the full dehydrogenase complex reaction
in which the ultimate electron acceptor is a disulfide (lipoyl/E3). The
DHTKD1 E1a subunit itself performs ThDP-dependent decarboxylation of
2-oxoadipate and transfers the acyl group to the E2 lipoyl moiety; the
more specific and accurate MF for DHTKD1 is GO:0160166 (2-oxoadipate
dehydrogenase activity), which is separately annotated with IDA support.
supported_by:
- reference_id: PMID:29191460
supporting_text: >-
It is involved in the oxidative decarboxylation of 2-oxoadipate (OA) to
glutaryl-CoA on the final degradative pathway of L-lysine
- term:
id: GO:0030976
label: thiamine pyrophosphate binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: >-
InterPro-based annotation of thiamine diphosphate (ThDP) binding. ThDP is
the essential catalytic cofactor of DHTKD1, confirmed biochemically and by
crystal structures of the DHTKD1-ThDP complex.
action: ACCEPT
reason: >-
DHTKD1 is a ThDP-dependent decarboxylase; ThDP is documented as its
cofactor (UniProt COFACTOR, PMID:32695416; DHTKD1-ThDP crystal structure
PMID:32633484). The InterPro TPP-binding domain (IPR011603/IPR029061) is
present. This is a core molecular function.
supported_by:
- reference_id: PMID:29191460
supporting_text: >-
Herein are reported unique properties of the novel human thiamin
diphosphate (ThDP)-dependent enzyme 2-oxoadipate dehydrogenase (hE1a)
- term:
id: GO:0160166
label: 2-oxoadipate dehydrogenase activity
evidence_type: IEA
original_reference_id: GO_REF:0000116
qualifier: enables
review:
summary: >-
RHEA-mapped IEA for the core catalytic activity of DHTKD1: the
ThDP-dependent oxidative decarboxylation of 2-oxoadipate (RHEA:69576).
This is the primary, experimentally validated molecular function.
action: ACCEPT
reason: >-
Matches the reaction assigned in UniProt (RHEA:69576) and is directly
supported by biochemistry (PMID:29191460, PMID:32633484) and structure.
Duplicate of the IDA-supported GO:0160166 below; both are correct.
supported_by:
- reference_id: PMID:29191460
supporting_text: >-
hE1a displays an approximately 49-fold preference in catalytic
efficiency for OA over OG, indicating that hE1a is specific to the
2-oxoadipate dehydrogenase complex
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:28514442
qualifier: enables
review:
summary: >-
High-throughput affinity-purification/mass-spectrometry interactome
(BioPlex 2.0) IPI to PGLYRP3 (Q96LB9). Bare "protein binding" is
uninformative about DHTKD1's molecular function.
action: MARK_AS_OVER_ANNOTATED
reason: >-
This is a proteome-scale AP-MS screen, not a directed study of DHTKD1's
biology; the recorded partner (PGLYRP3) has no established functional
relationship to 2-oxoadipate catabolism. Per curation guidance, bare
GO:0005515 protein binding IPIs are uninformative and are marked as
over-annotation rather than removed. The biologically meaningful
interaction of DHTKD1 is with the E2 subunit DLST, captured by the
oxoadipate dehydrogenase complex annotation.
supported_by:
- reference_id: PMID:28514442
supporting_text: >-
BioPlex 2.0 exceeds previous experimentally derived interaction networks
in depth and breadth
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:32296183
qualifier: enables
review:
summary: >-
Binary yeast-two-hybrid interactome (HuRI) IPI to an isoform of BMAL1
(O00327-8). Bare "protein binding" is uninformative about DHTKD1's
molecular function.
action: MARK_AS_OVER_ANNOTATED
reason: >-
This is a genome-scale binary interaction map, not a directed functional
study of DHTKD1. The reported partner has no established role in
2-oxoadipate/lysine catabolism. Per curation guidance, bare protein
binding IPIs are marked as over-annotation rather than removed.
supported_by:
- reference_id: PMID:32296183
supporting_text: A reference map of the human binary protein interactome.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:33961781
qualifier: enables
review:
summary: >-
High-throughput AP-MS interactome (BioPlex-derived, cell-specific
networks) IPI to PGLYRP3 (Q96LB9). Bare "protein binding" is
uninformative about DHTKD1's molecular function.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Proteome-scale interactome dataset rather than a directed DHTKD1 study;
the reported partner has no established connection to 2-oxoadipate
catabolism. Per curation guidance, bare protein binding IPIs are marked
as over-annotation rather than removed.
supported_by:
- reference_id: PMID:33961781
supporting_text: Dual proteome-scale networks reveal cell-specific remodeling
of the human interactome.
- term:
id: GO:0005759
label: mitochondrial matrix
evidence_type: IEA
original_reference_id: GO_REF:0000107
qualifier: is_active_in
review:
summary: >-
Orthology-based (Ensembl Compara) is_active_in annotation to the
mitochondrial matrix, transferred from mouse ortholog. Consistent with
the matrix localization of a soluble ThDP-dependent dehydrogenase.
action: ACCEPT
reason: >-
DHTKD1 has an N-terminal mitochondrial transit peptide and functions as a
soluble matrix enzyme of the OADHC; matrix localization is supported by
Reactome and by the shared architecture with the OGDH complex.
supported_by:
- reference_id: PMID:29191460
supporting_text: >-
the dihydrolipoyl succinyltransferase (hE2o) and the dihydrolipoyl
dehydrogenase (hE3) components of the tricarboxylic acid cycle
2-oxoglutarate dehydrogenase complex (OGDHc) for its activity
- term:
id: GO:0009063
label: amino acid catabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000107
qualifier: involved_in
review:
summary: >-
Orthology-based involvement in amino acid catabolism. Correct but a
generic parent of the specific L-lysine/L-tryptophan catabolic processes
DHTKD1 participates in.
action: KEEP_AS_NON_CORE
reason: >-
Accurate at a high level (DHTKD1 acts on the convergent 2-oxoadipate step
of lysine/hydroxylysine/tryptophan degradation) but subsumed by the more
specific L-lysine catabolic process (GO:0019477). Retained as non-core
background rather than as a distinct core function.
supported_by:
- reference_id: PMID:29191460
supporting_text: >-
on the final degradative pathway of L-lysine and is critical for
mitochondrial metabolism
- term:
id: GO:0019477
label: L-lysine catabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000107
qualifier: involved_in
review:
summary: >-
Orthology-based annotation to L-lysine catabolism. This is the principal
biological process in which DHTKD1 acts, catalyzing the final common
2-oxoadipate step of the lysine (and hydroxylysine/tryptophan)
degradation pathway.
action: ACCEPT
reason: >-
Well supported: DHTKD1 performs the rate-limiting decarboxylation of
2-oxoadipate, the convergent intermediate of L-lysine catabolism; disease
variants cause elevated 2-oxoadipate/2-aminoadipate. Core process.
supported_by:
- reference_id: PMID:29191460
supporting_text: >-
It is involved in the oxidative decarboxylation of 2-oxoadipate (OA) to
glutaryl-CoA on the final degradative pathway of L-lysine
- term:
id: GO:0005739
label: mitochondrion
evidence_type: IDA
original_reference_id: GO_REF:0000052
qualifier: located_in
review:
summary: >-
Immunofluorescence-based (HPA) IDA localizing DHTKD1 to the
mitochondrion. Consistent with all other evidence.
action: ACCEPT
reason: >-
Directly observed mitochondrial localization by immunofluorescence,
concordant with the mitochondrial matrix function of the OADHC E1a
subunit.
supported_by:
- reference_id: PMID:23141294
supporting_text: >-
implicating an important role for DHTKD1 in mitochondrial energy
production and neurological development.
- term:
id: GO:0005739
label: mitochondrion
evidence_type: HTP
original_reference_id: PMID:34800366
qualifier: located_in
review:
summary: >-
High-throughput mitochondrial proteomics (MitoCoP) detecting DHTKD1 in
the high-confidence human mitochondrial proteome.
action: ACCEPT
reason: >-
Independent proteomic confirmation of mitochondrial localization,
consistent with the transit peptide and matrix function.
supported_by:
- reference_id: PMID:34800366
supporting_text: >-
defined a mitochondrial high-confidence proteome of >1,100 proteins
(MitoCoP)
- term:
id: GO:0160166
label: 2-oxoadipate dehydrogenase activity
evidence_type: IDA
original_reference_id: PMID:29191460
qualifier: enables
review:
summary: >-
Direct biochemical demonstration that recombinant human E1a (DHTKD1)
oxidatively decarboxylates 2-oxoadipate, with ~49-fold catalytic
preference for 2-oxoadipate over 2-oxoglutarate. This is the defining,
experimentally validated molecular function of the gene.
action: ACCEPT
reason: >-
Gold-standard IDA evidence for the core catalytic activity; corroborated
by kinetics (KM 0.012-0.015 mM for 2-oxoadipate) and crystal structures
(PMID:32633484, PMID:32695416).
supported_by:
- reference_id: PMID:29191460
supporting_text: >-
hE1a displays an approximately 49-fold preference in catalytic
efficiency for OA over OG, indicating that hE1a is specific to the
2-oxoadipate dehydrogenase complex
- term:
id: GO:0160167
label: oxoadipate dehydrogenase complex
evidence_type: IDA
original_reference_id: PMID:29191460
qualifier: part_of
review:
summary: >-
DHTKD1 is the E1a subunit of the 2-oxoadipate dehydrogenase complex,
which it forms together with the shared E2 (DLST) and E3 (DLD) components
of the 2-oxoglutarate dehydrogenase machinery. Directly demonstrated by
reconstitution of an active complex.
action: ACCEPT
reason: >-
Core cellular-component annotation. DHTKD1 recruits E2 (DLST) and E3 (DLD)
to assemble a functional OADHC; the E1 subunit is complex-specific. This
is the biologically meaningful protein-protein assembly for DHTKD1.
supported_by:
- reference_id: PMID:29191460
supporting_text: >-
The hE1a has recruited the dihydrolipoyl succinyltransferase (hE2o) and
the dihydrolipoyl dehydrogenase (hE3) components of the tricarboxylic
acid cycle 2-oxoglutarate dehydrogenase complex (OGDHc) for its activity
- term:
id: GO:0005759
label: mitochondrial matrix
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9858321
qualifier: located_in
review:
summary: >-
Reactome TAS localizing the DHTKD1-catalyzed 2-oxoadipate decarboxylation
to the mitochondrial matrix, the compartment of the OADHC.
action: ACCEPT
reason: >-
Consistent with the soluble matrix location of the E1a subunit of the
OADHC and with orthology/proteomic evidence.
supported_by:
- reference_id: PMID:29191460
supporting_text: >-
the tricarboxylic acid cycle 2-oxoglutarate dehydrogenase complex
(OGDHc) for its activity
- term:
id: GO:0005759
label: mitochondrial matrix
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9858589
qualifier: located_in
review:
summary: >-
Reactome TAS localizing the OADHC E3 (DLD) dihydrolipoyl dehydrogenation
step to the mitochondrial matrix, the compartment where DHTKD1 acts.
action: ACCEPT
reason: >-
Matrix localization is well established for the OADHC in which DHTKD1 is
the E1 subunit.
supported_by:
- reference_id: PMID:29191460
supporting_text: >-
the dihydrolipoyl dehydrogenase (hE3) components of the tricarboxylic
acid cycle 2-oxoglutarate dehydrogenase complex (OGDHc) for its activity
- term:
id: GO:0005759
label: mitochondrial matrix
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9858590
qualifier: located_in
review:
summary: >-
Reactome TAS localizing the OADHC E2 (DLST) glutaryl transfer to CoA in
the mitochondrial matrix, the compartment where DHTKD1 acts.
action: ACCEPT
reason: >-
Consistent with matrix localization of the OADHC and of DHTKD1.
supported_by:
- reference_id: PMID:29191460
supporting_text: >-
the dihydrolipoyl succinyltransferase (hE2o) and the dihydrolipoyl
dehydrogenase (hE3) components of the tricarboxylic acid cycle
2-oxoglutarate dehydrogenase complex (OGDHc) for its activity
- term:
id: GO:0005739
label: mitochondrion
evidence_type: IDA
original_reference_id: PMID:23141294
qualifier: located_in
review:
summary: >-
IDA localizing DHTKD1 to the mitochondrion, from the study that
established the DHTKD1-CMT2 link and reported subcellular localization.
action: ACCEPT
reason: >-
Direct experimental evidence for mitochondrial localization (UniProt
SUBCELLULAR LOCATION cites this paper); concordant with all other data.
supported_by:
- reference_id: PMID:23141294
supporting_text: >-
implicating an important role for DHTKD1 in mitochondrial energy
production and neurological development.
- term:
id: GO:0006091
label: generation of precursor metabolites and energy
evidence_type: IMP
original_reference_id: PMID:23141294
qualifier: involved_in
review:
summary: >-
IMP from a DHTKD1-silencing study reporting decreased ATP and total
NAD(+)/NADH. This is a downstream physiological consequence of losing a
lysine-catabolic enzyme rather than a direct biological process of DHTKD1.
action: MARK_AS_OVER_ANNOTATED
reason: >-
DHTKD1 knockdown reduces cellular ATP/NAD(H) (an indirect metabolic
readout), but DHTKD1 is not part of primary energy-generating machinery
such as the TCA cycle or oxidative phosphorylation; its direct role is the
2-oxoadipate step of amino-acid (lysine/tryptophan) catabolism. This term
over-generalizes a secondary phenotype. Note this contrasts with the OGDH
paralog, which is a bona fide TCA-cycle energy enzyme. Retained (not
removed) as it derives from an experimental IMP.
supported_by:
- reference_id: PMID:23141294
supporting_text: >-
DHTKD1 silencing was found to lead to impaired energy production,
evidenced by decreased ATP, total NAD(+) and NADH, and NADH levels
- term:
id: GO:0006569
label: L-tryptophan catabolic process
evidence_type: IEA
original_reference_id: PMID:29191460
qualifier: involved_in
review:
summary: >-
Proposed additional biological-process annotation. 2-oxoadipate is the
convergent intermediate of L-lysine, L-hydroxylysine AND L-tryptophan
catabolism; by decarboxylating 2-oxoadipate, DHTKD1 catalyzes the final
common step of the tryptophan degradation pathway as well as the lysine
pathway.
action: NEW
reason: >-
UniProt explicitly states DHTKD1 is responsible for the last step of
L-lysine, L-hydroxylysine and L-tryptophan catabolism (common product
2-oxoadipate). The tryptophan-catabolic role is not otherwise captured in
GOA and complements the existing L-lysine catabolic process annotation.
supported_by:
- reference_id: PMID:29191460
supporting_text: >-
It is involved in the oxidative decarboxylation of 2-oxoadipate (OA) to
glutaryl-CoA on the final degradative pathway of L-lysine
core_functions:
- description: >-
Thiamine diphosphate-dependent 2-oxoadipate dehydrogenase (E1a) activity: the
first, rate-limiting oxidative decarboxylation step of the mitochondrial
2-oxoadipate dehydrogenase complex, acting on the L-lysine/L-hydroxylysine/
L-tryptophan catabolic pathway.
molecular_function:
id: GO:0160166
label: 2-oxoadipate dehydrogenase activity
directly_involved_in:
- id: GO:0019477
label: L-lysine catabolic process
- id: GO:0006569
label: L-tryptophan catabolic process
locations:
- id: GO:0005759
label: mitochondrial matrix
in_complex:
id: GO:0160167
label: oxoadipate dehydrogenase complex
supported_by:
- reference_id: PMID:29191460
supporting_text: >-
It is involved in the oxidative decarboxylation of 2-oxoadipate (OA) to
glutaryl-CoA on the final degradative pathway of L-lysine
- reference_id: PMID:29191460
supporting_text: >-
hE1a displays an approximately 49-fold preference in catalytic efficiency
for OA over OG, indicating that hE1a is specific to the 2-oxoadipate
dehydrogenase complex
- description: >-
Thiamine diphosphate cofactor binding required for the decarboxylase activity
of the E1a subunit.
molecular_function:
id: GO:0030976
label: thiamine pyrophosphate binding
locations:
- id: GO:0005759
label: mitochondrial matrix
supported_by:
- reference_id: PMID:29191460
supporting_text: >-
Herein are reported unique properties of the novel human thiamin
diphosphate (ThDP)-dependent enzyme 2-oxoadipate dehydrogenase (hE1a)
proposed_new_terms: []
suggested_questions:
- question: >-
Given that DHTKD1 shares E2 (DLST) and E3 (DLD) with the 2-oxoglutarate
dehydrogenase complex, how is flux partitioned between the OGDHC and OADHC in
tissues where both are expressed (e.g. liver)?
- question: >-
Why is alpha-aminoadipic/alpha-ketoadipic aciduria caused by DHTKD1 loss so
frequently asymptomatic, and what genetic or metabolic factors modify the
CMT2Q neuropathy phenotype?
suggested_experiments:
- description: >-
Tissue-resolved metabolic flux analysis (e.g. 13C-lysine tracing) in
DHTKD1-knockout versus wild-type cells to quantify the contribution of DHTKD1
to 2-oxoadipate turnover and downstream glutaryl-CoA and energy metabolism.
hypothesis: >-
DHTKD1 loss diverts 2-oxoadipate away from glutaryl-CoA, causing measurable
accumulation of 2-oxoadipate/2-aminoadipate without major bioenergetic deficit.
- description: >-
Structural and kinetic characterization of the assembled DHTKD1-DLST-DLD
megacomplex to define substrate channeling and the effect of AAKAD variants
(e.g. G729R, R715C) on complex assembly and activity.
hypothesis: >-
AAKAD-causing variants impair DHTKD1-DLST assembly, disrupting intermediate
channeling rather than abolishing intrinsic decarboxylase chemistry.
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO
terms
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: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:23141294
title: A nonsense mutation in DHTKD1 causes Charcot-Marie-Tooth disease type 2 in
a large Chinese pedigree.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
PubMed-verified. Establishes DHTKD1 loss-of-function in CMT2Q and reports
mitochondrial localization and impaired ATP/NAD(H) on silencing. Cited
correctly for the mitochondrion (IDA) and energy (IMP) annotations.
- id: PMID:28514442
title: Architecture of the human interactome defines protein communities and disease
networks.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
BioPlex 2.0 AP-MS interactome. Correctly cited as the source of a
high-throughput protein-binding IPI, but not a directed study of DHTKD1
function; the recorded partner is not functionally informative.
- id: PMID:29191460
title: The mitochondrial 2-oxoadipate and 2-oxoglutarate dehydrogenase complexes
share their E2 and E3 components for their function and both generate reactive
oxygen species.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Primary biochemical characterization of human E1a (DHTKD1): ThDP-dependent
2-oxoadipate decarboxylation, ~49x preference for 2-oxoadipate over
2-oxoglutarate, and recruitment of shared E2/E3. Anchors the core MF and
complex annotations.
- id: PMID:32296183
title: A reference map of the human binary protein interactome.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
HuRI binary Y2H interactome. Source of a high-throughput protein-binding
IPI; not a directed DHTKD1 study and functionally uninformative for this
gene.
- id: PMID:33961781
title: Dual proteome-scale networks reveal cell-specific remodeling of the human
interactome.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
BioPlex-derived proteome-scale interactome. Source of a high-throughput
protein-binding IPI; not functionally informative for DHTKD1.
- id: PMID:34800366
title: Quantitative high-confidence human mitochondrial proteome and its dynamics
in cellular context.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
MitoCoP high-confidence mitochondrial proteome; independently confirms
DHTKD1 mitochondrial localization.
- id: Reactome:R-HSA-9858321
title: DHTKD1 dimer decarboxylates 2-OA
findings: []
- id: Reactome:R-HSA-9858589
title: DLD dimer dehydrogenates dihydrolipoyl
findings: []
- id: Reactome:R-HSA-9858590
title: DLST transfers glutaryl to CoA
findings: []