HOGA1 (4-hydroxy-2-oxoglutarate aldolase, mitochondrial; EC 4.1.3.16; formerly DHDPSL/C10orf65) is a mitochondrial matrix enzyme that catalyzes the final step of the hydroxyproline (4-hydroxyproline) degradation pathway, performing the retro-aldol cleavage of 4-hydroxy-2-oxoglutarate (HOG) into glyoxylate and pyruvate. It belongs to the dihydrodipicolinate synthase (DapA/DHDPS) family and functions as a Schiff-base (type I) aldolase, using an active-site lysine (Lys196) as the catalytic nucleophile; the enzyme is active against both the (4R) and (4S) enantiomers of HOG. The mature protein, produced after cleavage of an N-terminal mitochondrial transit peptide, assembles into a homotetramer (dimer of dimers). HOGA1 is expressed most highly in kidney and liver, the principal sites of hydroxyproline turnover. Loss-of-function variants cause primary hyperoxaluria type 3 (PH3/HP3), an autosomal-recessive disorder of endogenous oxalate synthesis characterized by calcium oxalate urolithiasis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0008700
(R,S)-4-hydroxy-2-oxoglutarate aldolase activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetically-inferred core molecular function. This is the enzyme's defining activity, directly confirmed for the human protein by structural and kinetic study.
Reason: This is the precise, correct molecular function of HOGA1, supported by direct biochemical characterization of the recombinant human enzyme and matching the IDA annotation from PMID:21998747. The IBA call is at the right level of specificity and represents the core function.
Supporting Evidence:
PMID:21998747
The activity of recombinant hHOGA proves that it is indeed the aldolase identified in the genomic analysis of PH3 patients.
|
|
GO:0005739
mitochondrion
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetically-inferred mitochondrial localization, consistent with the N-terminal mitochondrial transit peptide and the ortholog-based subcellular location.
Reason: HOGA1 carries an N-terminal mitochondrial transit peptide (residues 1-25) and is a mitochondrial-matrix enzyme; the IBA is-active-in mitochondrion annotation is correct.
Supporting Evidence:
file:human/HOGA1/HOGA1-uniprot.txt
Mitochondrion {ECO:0000250|UniProtKB:Q0P5I5}
|
|
GO:0009436
glyoxylate catabolic process
|
IBA
GO_REF:0000033 |
KEEP AS NON CORE |
Summary: Phylogenetically-inferred participation in glyoxylate metabolism. HOGA1 is a mitochondrial glyoxylate-generating enzyme in the hydroxyproline degradation pathway.
Reason: HOGA1 participates in mitochondrial glyoxylate metabolism, producing glyoxylate as a product of HOG cleavage. Note that HOGA1 generates rather than degrades glyoxylate, so "glyoxylate catabolic process" is a somewhat imperfect descriptor of its direct role; however it is the standard consortium call for the hydroxyproline/glyoxylate pathway and is not wrong at the pathway level. The core BP is hydroxyproline catabolism; retain this as a non-core pathway-participation annotation.
Supporting Evidence:
PMID:21998747
In the terminal reaction, HOG is cleaved by HOGA to produce pyruvate and glyoxylate.
|
|
GO:0005739
mitochondrion
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic mitochondrial localization from UniProt SubCell/ARBA, consistent with the transit peptide and experimental data.
Reason: Correct localization supported by the mitochondrial targeting sequence and multiple experimental/orthology-based annotations.
Supporting Evidence:
file:human/HOGA1/HOGA1-uniprot.txt
Mitochondrion {ECO:0000250|UniProtKB:Q0P5I5}
|
|
GO:0008700
(R,S)-4-hydroxy-2-oxoglutarate aldolase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic annotation of the core aldolase activity from the ARBA/RHEA/EC mapping (EC 4.1.3.16, RHEA:30687).
Reason: Correct core molecular function, redundant with and consistent with the IBA and IDA annotations to the same term. EC 4.1.3.16 is the enzyme's assigned EC number.
Supporting Evidence:
PMID:21998747
hHOGA performs a retro-aldol cleavage reaction reminiscent of the trimeric 2-keto-3-deoxy-6-phosphogluconate aldolases.
|
|
GO:0009436
glyoxylate catabolic process
|
IEA
GO_REF:0000117 |
KEEP AS NON CORE |
Summary: Electronic (ARBA) annotation to glyoxylate catabolic process, duplicating the IBA/IMP calls to the same term.
Reason: Same reasoning as the IBA glyoxylate catabolic process annotation - a valid pathway-participation term but not the core BP (which is hydroxyproline catabolism). Keep as non-core.
Supporting Evidence:
PMID:21998747
In the terminal reaction, HOG is cleaved by HOGA to produce pyruvate and glyoxylate.
|
|
GO:0016829
lyase activity
|
IEA
GO_REF:0000002 |
MARK AS OVER ANNOTATED |
Summary: InterPro2GO electronic annotation to the broad parent term lyase activity, based on the DapA-like domain.
Reason: "lyase activity" is a correct but uninformatively general ancestor of the specific molecular function (GO:0008700, an aldolase, which is a carbon-carbon lyase). It is subsumed by the more precise aldolase-activity annotations and adds no information; mark as over-annotated rather than removed since it is not wrong.
Supporting Evidence:
PMID:21998747
hHOGA performs a retro-aldol cleavage reaction reminiscent of the trimeric 2-keto-3-deoxy-6-phosphogluconate aldolases.
|
|
GO:0106009
(4S)-4-hydroxy-2-oxoglutarate aldolase activity
|
IEA
GO_REF:0000116 |
ACCEPT |
Summary: RHEA-based electronic annotation of the (4S)-stereospecific aldolase activity (RHEA:35639).
Reason: HOGA1 cleaves the (4S) enantiomer of HOG (RHEA:35639), so this stereospecific child term is correct. The enzyme also acts on the (4R) form, hence the broader (R,S) term GO:0008700 is retained as the primary MF; both are legitimate.
Supporting Evidence:
PMID:21998747
Previous studies have shown that the bovine kidney, bovine liver, and rat liver enzymes have equal activity against the R- and S-forms of HOG
|
|
GO:0005515
protein binding
|
IPI
PMID:27499296 Mitochondrial Protein Interaction Mapping Identifies Regulat... |
MARK AS OVER ANNOTATED |
Summary: High-throughput mitochondrial protein-interaction screen; captured interaction with STARD7 (Q9NQZ5). Uninformative bare "protein binding" term.
Reason: "protein binding" (GO:0005515) is an uninformative molecular-function term that does not describe HOGA1's activity. This IPI derives from a large-scale mitochondrial protein-interaction mapping study, with no evidence that the interaction is functionally relevant to the aldolase. Per curation policy, bare protein-binding IPIs are marked as over-annotated rather than removed.
Supporting Evidence:
PMID:27499296
Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function.
|
|
GO:0005515
protein binding
|
IPI
PMID:28514442 Architecture of the human interactome defines protein commun... |
MARK AS OVER ANNOTATED |
Summary: High-throughput affinity-purification interactome screen (BioPlex); captured interaction with USP47 (Q96K76). Uninformative bare "protein binding" term.
Reason: Uninformative "protein binding" term from a proteome-scale interactome dataset, with no evidence of functional relevance to HOGA1's catalytic role. Marked as over-annotated per policy on bare protein-binding IPIs.
Supporting Evidence:
PMID:28514442
Architecture of the human interactome defines protein communities and disease networks.
|
|
GO:0005515
protein binding
|
IPI
PMID:32296183 A reference map of the human binary protein interactome. |
MARK AS OVER ANNOTATED |
Summary: High-throughput binary (Y2H) interactome screen (HuRI); captured interaction with CIMAP1A (Q96PU9). Uninformative bare "protein binding" term.
Reason: Uninformative "protein binding" term from a systematic binary-interactome map, with no evidence of functional relevance to the aldolase activity. Marked as over-annotated per policy on bare protein-binding IPIs.
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 affinity-purification interactome screen (BioPlex 3.0); captured interaction with USP47 (Q96K76). Uninformative bare "protein binding" term.
Reason: Uninformative "protein binding" term from a proteome-scale interactome dataset, duplicating the other HT interaction annotations. Marked as over-annotated per policy on bare protein-binding IPIs.
Supporting Evidence:
PMID:33961781
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
|
|
GO:0005739
mitochondrion
|
HTP
PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... |
ACCEPT |
Summary: High-throughput identification of HOGA1 in the high-confidence human mitochondrial proteome.
Reason: Independent proteomic evidence for mitochondrial localization, consistent with the transit peptide and all other localization annotations.
Supporting Evidence:
PMID:34800366
Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context.
|
|
GO:0005739
mitochondrion
|
ISS
GO_REF:0000024 |
ACCEPT |
Summary: Sequence-similarity transfer of mitochondrial localization from the bovine ortholog (Q0P5I5).
Reason: Correct localization; the bovine ortholog was purified from kidney mitochondria and human HOGA1 has the corresponding transit peptide.
Supporting Evidence:
PMID:21998747
mitochondrial enzyme purified from bovine kidney
|
|
GO:0005759
mitochondrial matrix
|
TAS
Reactome:R-HSA-6784423 |
ACCEPT |
Summary: Reactome-curated localization of the HOGA1-catalyzed HOG cleavage reaction to the mitochondrial matrix.
Reason: Mitochondrial matrix is the precise sub-compartment for this soluble matrix aldolase; more specific than "mitochondrion" and consistent with the pathway context. This is the best cellular-component term.
Supporting Evidence:
Reactome:R-HSA-6784423
aldol-cleaves 4-OH-2-oxoglutarate (HOG) to glyoxylate and pyruvate
|
|
GO:0005739
mitochondrion
|
ISS
PMID:21998747 Structural and biochemical studies of human 4-hydroxy-2-oxog... |
ACCEPT |
Summary: Sequence-similarity-based mitochondrial localization annotation (BHF-UCL), referencing the structural/biochemical paper and bovine ortholog.
Reason: Correct mitochondrial localization; the human enzyme was characterized from the mitochondrial hydroxyproline pathway and the bovine ortholog was purified from kidney mitochondria.
Supporting Evidence:
PMID:21998747
mitochondrial enzyme purified from bovine kidney
|
|
GO:0008700
(R,S)-4-hydroxy-2-oxoglutarate aldolase activity
|
IDA
PMID:21998747 Structural and biochemical studies of human 4-hydroxy-2-oxog... |
ACCEPT |
Summary: Direct assay of recombinant human HOGA1 aldolase activity, including crystal structure, catalytic-residue mutagenesis (Lys196, Tyr168), and kinetics.
Reason: This is the definitive experimental demonstration of HOGA1's core molecular function. Recombinant human enzyme performs retro-aldol cleavage of HOG; catalytic mutants (K196A, Y168F) abolish activity, establishing the mechanism. Core function.
Supporting Evidence:
PMID:21998747
The Y168F and K196A hHOGA variants exhibited no enzymatic activity
PMID:21998747
The activity of recombinant hHOGA proves that it is indeed the aldolase identified in the genomic analysis of PH3 patients.
|
|
GO:0019470
trans-4-hydroxy-L-proline catabolic process
|
IDA
PMID:21998747 Structural and biochemical studies of human 4-hydroxy-2-oxog... |
ACCEPT |
Summary: HOGA1 catalyzes the terminal (final) step of the four-enzyme mitochondrial hydroxyproline degradation pathway.
Reason: This is the core biological process for HOGA1. The enzyme catalyzes the terminal step of 4-hydroxyproline catabolism, and UniProt describes its function as catalyzing the final step in the metabolic pathway of hydroxyproline.
Supporting Evidence:
PMID:21998747
The degradation pathway for 4-Hyp (Figure 1) involves the step-wise action of four mitochondrial enzymes
file:human/HOGA1/HOGA1-uniprot.txt
Catalyzes the final step in the metabolic pathway of
|
|
GO:0033609
oxalate metabolic process
|
IMP
PMID:21896830 Primary hyperoxaluria type III gene HOGA1 (formerly DHDPSL) ... |
KEEP AS NON CORE |
Summary: HOGA1 variants influence urinary oxalate; loss-of-function mutations cause primary hyperoxaluria type 3, linking HOGA1 function to oxalate homeostasis.
Reason: The connection to oxalate metabolism is real but indirect - HOGA1 does not act on oxalate directly; rather, its dysfunction perturbs glyoxylate/oxalate handling and causes hyperoxaluria (PH3). This is a disease-level/physiological link rather than the enzyme's direct catalytic role, so keep as non-core.
Supporting Evidence:
PMID:21896830
hypothesized to cause a gain of mitochondrial 4-hydroxy-2-oxoglutarate aldolase
PMID:21896830
HOGA1 may be a predisposing factor for this
|
|
GO:0042803
protein homodimerization activity
|
IDA
PMID:21998747 Structural and biochemical studies of human 4-hydroxy-2-oxog... |
ACCEPT |
Summary: Structural study shows HOGA1 assembles via a "tight" dimer interface into a homotetramer (dimer of dimers); the active site lies at the dimer interface.
Reason: The crystal structure directly demonstrates self-association. The biological assembly is a homotetramer, but it is built as a dimer of dimers, and the active site is formed at the tight dimer interface (a residue from the adjacent monomer, Tyr140', contributes to the active site), so homodimerization is a genuine, structurally-supported self-association activity. UniProt records the assembly as a homotetramer.
Supporting Evidence:
PMID:21998747
reveal a tetrameric structure composed of a dimer of dimers
file:human/HOGA1/HOGA1-uniprot.txt
SUBUNIT: Homotetramer
|
|
GO:0042866
pyruvate biosynthetic process
|
IDA
PMID:21998747 Structural and biochemical studies of human 4-hydroxy-2-oxog... |
KEEP AS NON CORE |
Summary: Pyruvate is a co-product of the HOGA1-catalyzed cleavage of HOG (HOG -> glyoxylate + pyruvate).
Reason: Pyruvate is genuinely produced by the HOGA1 reaction, so this annotation is factually correct. However, pyruvate is a minor co-product of hydroxyproline catabolism and HOGA1 is not a dedicated pyruvate-biosynthetic enzyme; keep as a non-core annotation rather than a core function.
Supporting Evidence:
PMID:21998747
In the terminal reaction, HOG is cleaved by HOGA to produce pyruvate and glyoxylate.
|
|
GO:0046487
glyoxylate metabolic process
|
IDA
PMID:21998747 Structural and biochemical studies of human 4-hydroxy-2-oxog... |
KEEP AS NON CORE |
Summary: HOGA1 produces glyoxylate as a product of HOG cleavage, participating in mitochondrial glyoxylate metabolism.
Reason: Correct - HOGA1 generates glyoxylate, so it participates in glyoxylate metabolic process. This is a more accurate parent than "glyoxylate catabolic process" (since HOGA1 makes, not degrades, glyoxylate), but it is a downstream/pathway annotation rather than the core hydroxyproline-catabolic function; keep as non-core.
Supporting Evidence:
PMID:21998747
In the terminal reaction, HOG is cleaved by HOGA to produce pyruvate and glyoxylate.
|
|
GO:0009436
glyoxylate catabolic process
|
IMP
PMID:20797690 Mutations in DHDPSL are responsible for primary hyperoxaluri... |
KEEP AS NON CORE |
Summary: Mutations in HOGA1 (DHDPSL) cause primary hyperoxaluria type 3, establishing HOGA1's role in the glyoxylate/hydroxyproline pathway by loss of function.
Reason: The disease-based IMP correctly places HOGA1 in the glyoxylate pathway, but "glyoxylate catabolic process" is an imperfect descriptor since HOGA1 produces rather than degrades glyoxylate; the core BP is hydroxyproline catabolism. Retain as a non-core pathway-participation annotation.
Supporting Evidence:
PMID:20797690
cause a third type of PH (PH III)
PMID:20797690
the gene encoding 4-hydroxy-2-oxoglutarate
|
|
GO:0008700
(R,S)-4-hydroxy-2-oxoglutarate aldolase activity
|
ISS
GO_REF:0000024 |
ACCEPT |
Summary: Sequence-similarity transfer of the core aldolase activity from the bovine ortholog (Q0P5I5), which shares ~90% identity with human HOGA1.
Reason: Correct core molecular function, redundant with the direct experimental (IDA) annotation to the same term. The bovine ortholog is 90.2% identical and functionally characterized.
Supporting Evidence:
PMID:21998747
Sequence comparison of human HOGA with bovine HOGA (90.2% identity)
|
Q: Given that HOGA1 produces glyoxylate (an oxalate precursor), what is the precise mechanism by which HOGA1 loss-of-function causes hyperoxaluria in PH3 - accumulation of HOG or upstream intermediates, dominant-negative effects, or dysregulation of glyoxylate detoxification?
Experiment: Metabolomic quantification of HOG, glyoxylate, and oxalate in HOGA1-deficient versus wild-type hepatocyte/renal models to test whether HOG accumulation (rather than loss of glyoxylate production) drives the hyperoxaluric phenotype.
HOGA1 = 4-hydroxy-2-oxoglutarate aldolase, mitochondrial (EC 4.1.3.16; formerly DHDPSL /
C10orf65). Mitochondrial matrix enzyme catalysing the terminal step of the hydroxyproline
(4-Hyp) degradation pathway: retro-aldol cleavage of 4-hydroxy-2-oxoglutarate (HOG) into
glyoxylate + pyruvate. Belongs to the DapA (dihydrodipicolinate synthase, DHDPS) family;
Schiff-base type I aldolase using Lys196 as the catalytic nucleophile. Forms a homotetramer
(dimer of dimers). Loss-of-function mutations cause primary hyperoxaluria type 3 (PH3 /
HP3, MIM 613616).
Key point on directionality of disease: HOGA1 itself produces glyoxylate (a precursor of
oxalate), yet its loss causes hyperoxaluria. Mechanism is debated (loss-of-function with
accumulation of HOG/upstream intermediates that dysregulate glyoxylate detoxification /
possible dominant-negative effect), but the enzymatic reaction and the disease association
are both firmly established.
Four IPI GO:0005515 "protein binding" annotations from high-throughput interactome / mito
protein-interaction screens (PMID:27499296 STARD7; PMID:28514442 & 33961781 USP47;
PMID:32296183 CIMAP1A). Bare "protein binding" is uninformative and these are HT screens;
per policy -> MARK_AS_OVER_ANNOTATED (do NOT REMOVE bare protein-binding IPIs). No evidence
these interactions are functionally relevant to the aldolase activity.
Correct but very general parent of the specific aldolase MF -> MARK_AS_OVER_ANNOTATED
(redundant with GO:0008700). Not wrong.
PH3 / HP3 (MIM 613616): PMID:20797690. Loss-of-function mechanism supported
PMID:21896830.
falcon deep-research provider is out of credits (HTTP 402); no -deep-research-falcon.md
generated. Review grounded in UniProt Q86XE5, seeded GOA, and cached publications
(PMID:20797690, 21896830, 21998747) plus Reactome R-HSA-6784423.
id: Q86XE5
gene_symbol: HOGA1
product_type: PROTEIN
status: INITIALIZED
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: HOGA1 (4-hydroxy-2-oxoglutarate aldolase, mitochondrial; EC 4.1.3.16;
formerly DHDPSL/C10orf65) is a mitochondrial matrix enzyme that catalyzes the final
step of the hydroxyproline (4-hydroxyproline) degradation pathway, performing the
retro-aldol cleavage of 4-hydroxy-2-oxoglutarate (HOG) into glyoxylate and pyruvate.
It belongs to the dihydrodipicolinate synthase (DapA/DHDPS) family and functions
as a Schiff-base (type I) aldolase, using an active-site lysine (Lys196) as the
catalytic nucleophile; the enzyme is active against both the (4R) and (4S) enantiomers
of HOG. The mature protein, produced after cleavage of an N-terminal mitochondrial
transit peptide, assembles into a homotetramer (dimer of dimers). HOGA1 is expressed
most highly in kidney and liver, the principal sites of hydroxyproline turnover.
Loss-of-function variants cause primary hyperoxaluria type 3 (PH3/HP3), an autosomal-recessive
disorder of endogenous oxalate synthesis characterized by calcium oxalate urolithiasis.
existing_annotations:
- term:
id: GO:0008700
label: (R,S)-4-hydroxy-2-oxoglutarate aldolase activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: Phylogenetically-inferred core molecular function. This is the enzyme's
defining activity, directly confirmed for the human protein by structural and
kinetic study.
action: ACCEPT
reason: This is the precise, correct molecular function of HOGA1, supported by
direct biochemical characterization of the recombinant human enzyme and matching
the IDA annotation from PMID:21998747. The IBA call is at the right level of
specificity and represents the core function.
supported_by:
- reference_id: PMID:21998747
supporting_text: The activity of recombinant hHOGA proves that it is indeed
the aldolase identified in the genomic analysis of PH3 patients.
- term:
id: GO:0005739
label: mitochondrion
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: is_active_in
review:
summary: Phylogenetically-inferred mitochondrial localization, consistent with
the N-terminal mitochondrial transit peptide and the ortholog-based subcellular
location.
action: ACCEPT
reason: HOGA1 carries an N-terminal mitochondrial transit peptide (residues 1-25)
and is a mitochondrial-matrix enzyme; the IBA is-active-in mitochondrion annotation
is correct.
supported_by:
- reference_id: file:human/HOGA1/HOGA1-uniprot.txt
supporting_text: Mitochondrion {ECO:0000250|UniProtKB:Q0P5I5}
- term:
id: GO:0009436
label: glyoxylate catabolic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: Phylogenetically-inferred participation in glyoxylate metabolism. HOGA1
is a mitochondrial glyoxylate-generating enzyme in the hydroxyproline degradation
pathway.
action: KEEP_AS_NON_CORE
reason: HOGA1 participates in mitochondrial glyoxylate metabolism, producing glyoxylate
as a product of HOG cleavage. Note that HOGA1 generates rather than degrades
glyoxylate, so "glyoxylate catabolic process" is a somewhat imperfect descriptor
of its direct role; however it is the standard consortium call for the hydroxyproline/glyoxylate
pathway and is not wrong at the pathway level. The core BP is hydroxyproline
catabolism; retain this as a non-core pathway-participation annotation.
supported_by:
- reference_id: PMID:21998747
supporting_text: In the terminal reaction, HOG is cleaved by HOGA to produce
pyruvate and glyoxylate.
- term:
id: GO:0005739
label: mitochondrion
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: located_in
review:
summary: Electronic mitochondrial localization from UniProt SubCell/ARBA, consistent
with the transit peptide and experimental data.
action: ACCEPT
reason: Correct localization supported by the mitochondrial targeting sequence
and multiple experimental/orthology-based annotations.
supported_by:
- reference_id: file:human/HOGA1/HOGA1-uniprot.txt
supporting_text: Mitochondrion {ECO:0000250|UniProtKB:Q0P5I5}
- term:
id: GO:0008700
label: (R,S)-4-hydroxy-2-oxoglutarate aldolase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: Electronic annotation of the core aldolase activity from the ARBA/RHEA/EC
mapping (EC 4.1.3.16, RHEA:30687).
action: ACCEPT
reason: Correct core molecular function, redundant with and consistent with the
IBA and IDA annotations to the same term. EC 4.1.3.16 is the enzyme's assigned
EC number.
supported_by:
- reference_id: PMID:21998747
supporting_text: hHOGA performs a retro-aldol cleavage reaction reminiscent of
the trimeric 2-keto-3-deoxy-6-phosphogluconate aldolases.
- term:
id: GO:0009436
label: glyoxylate catabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000117
qualifier: involved_in
review:
summary: Electronic (ARBA) annotation to glyoxylate catabolic process, duplicating
the IBA/IMP calls to the same term.
action: KEEP_AS_NON_CORE
reason: Same reasoning as the IBA glyoxylate catabolic process annotation - a
valid pathway-participation term but not the core BP (which is hydroxyproline
catabolism). Keep as non-core.
supported_by:
- reference_id: PMID:21998747
supporting_text: In the terminal reaction, HOG is cleaved by HOGA to produce
pyruvate and glyoxylate.
- term:
id: GO:0016829
label: lyase activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: InterPro2GO electronic annotation to the broad parent term lyase activity,
based on the DapA-like domain.
action: MARK_AS_OVER_ANNOTATED
reason: "\"lyase activity\" is a correct but uninformatively general ancestor of\
\ the specific molecular function (GO:0008700, an aldolase, which is a carbon-carbon\
\ lyase). It is subsumed by the more precise aldolase-activity annotations and\
\ adds no information; mark as over-annotated rather than removed since it is\
\ not wrong."
supported_by:
- reference_id: PMID:21998747
supporting_text: hHOGA performs a retro-aldol cleavage reaction reminiscent of
the trimeric 2-keto-3-deoxy-6-phosphogluconate aldolases.
- term:
id: GO:0106009
label: (4S)-4-hydroxy-2-oxoglutarate aldolase activity
evidence_type: IEA
original_reference_id: GO_REF:0000116
qualifier: enables
review:
summary: RHEA-based electronic annotation of the (4S)-stereospecific aldolase
activity (RHEA:35639).
action: ACCEPT
reason: HOGA1 cleaves the (4S) enantiomer of HOG (RHEA:35639), so this stereospecific
child term is correct. The enzyme also acts on the (4R) form, hence the broader
(R,S) term GO:0008700 is retained as the primary MF; both are legitimate.
supported_by:
- reference_id: PMID:21998747
supporting_text: Previous studies have shown that the bovine kidney, bovine liver,
and rat liver enzymes have equal activity against the R- and S-forms of HOG
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:27499296
qualifier: enables
review:
summary: High-throughput mitochondrial protein-interaction screen; captured interaction
with STARD7 (Q9NQZ5). Uninformative bare "protein binding" term.
action: MARK_AS_OVER_ANNOTATED
reason: "\"protein binding\" (GO:0005515) is an uninformative molecular-function\
\ term that does not describe HOGA1's activity. This IPI derives from a large-scale\
\ mitochondrial protein-interaction mapping study, with no evidence that the\
\ interaction is functionally relevant to the aldolase. Per curation policy,\
\ bare protein-binding IPIs are marked as over-annotated rather than removed."
supported_by:
- reference_id: PMID:27499296
supporting_text: Mitochondrial Protein Interaction Mapping Identifies Regulators
of Respiratory Chain Function.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:28514442
qualifier: enables
review:
summary: High-throughput affinity-purification interactome screen (BioPlex); captured
interaction with USP47 (Q96K76). Uninformative bare "protein binding" term.
action: MARK_AS_OVER_ANNOTATED
reason: Uninformative "protein binding" term from a proteome-scale interactome
dataset, with no evidence of functional relevance to HOGA1's catalytic role.
Marked as over-annotated per policy on bare protein-binding IPIs.
supported_by:
- reference_id: PMID:28514442
supporting_text: Architecture of the human interactome defines protein communities
and disease networks.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:32296183
qualifier: enables
review:
summary: High-throughput binary (Y2H) interactome screen (HuRI); captured interaction
with CIMAP1A (Q96PU9). Uninformative bare "protein binding" term.
action: MARK_AS_OVER_ANNOTATED
reason: Uninformative "protein binding" term from a systematic binary-interactome
map, with no evidence of functional relevance to the aldolase activity. Marked
as over-annotated per policy on bare protein-binding IPIs.
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 affinity-purification interactome screen (BioPlex 3.0);
captured interaction with USP47 (Q96K76). Uninformative bare "protein binding"
term.
action: MARK_AS_OVER_ANNOTATED
reason: Uninformative "protein binding" term from a proteome-scale interactome
dataset, duplicating the other HT interaction annotations. Marked as over-annotated
per policy on bare protein-binding IPIs.
supported_by:
- reference_id: PMID:33961781
supporting_text: Dual proteome-scale networks reveal cell-specific remodeling
of the human interactome.
- term:
id: GO:0005739
label: mitochondrion
evidence_type: HTP
original_reference_id: PMID:34800366
qualifier: located_in
review:
summary: High-throughput identification of HOGA1 in the high-confidence human
mitochondrial proteome.
action: ACCEPT
reason: Independent proteomic evidence for mitochondrial localization, consistent
with the transit peptide and all other localization annotations.
supported_by:
- reference_id: PMID:34800366
supporting_text: Quantitative high-confidence human mitochondrial proteome and
its dynamics in cellular context.
- term:
id: GO:0005739
label: mitochondrion
evidence_type: ISS
original_reference_id: GO_REF:0000024
qualifier: located_in
review:
summary: Sequence-similarity transfer of mitochondrial localization from the bovine
ortholog (Q0P5I5).
action: ACCEPT
reason: Correct localization; the bovine ortholog was purified from kidney mitochondria
and human HOGA1 has the corresponding transit peptide.
supported_by:
- reference_id: PMID:21998747
supporting_text: mitochondrial enzyme purified from bovine kidney
- term:
id: GO:0005759
label: mitochondrial matrix
evidence_type: TAS
original_reference_id: Reactome:R-HSA-6784423
qualifier: located_in
review:
summary: Reactome-curated localization of the HOGA1-catalyzed HOG cleavage reaction
to the mitochondrial matrix.
action: ACCEPT
reason: Mitochondrial matrix is the precise sub-compartment for this soluble matrix
aldolase; more specific than "mitochondrion" and consistent with the pathway
context. This is the best cellular-component term.
supported_by:
- reference_id: Reactome:R-HSA-6784423
supporting_text: aldol-cleaves 4-OH-2-oxoglutarate (HOG) to glyoxylate and pyruvate
- term:
id: GO:0005739
label: mitochondrion
evidence_type: ISS
original_reference_id: PMID:21998747
qualifier: located_in
review:
summary: Sequence-similarity-based mitochondrial localization annotation (BHF-UCL),
referencing the structural/biochemical paper and bovine ortholog.
action: ACCEPT
reason: Correct mitochondrial localization; the human enzyme was characterized
from the mitochondrial hydroxyproline pathway and the bovine ortholog was purified
from kidney mitochondria.
supported_by:
- reference_id: PMID:21998747
supporting_text: mitochondrial enzyme purified from bovine kidney
- term:
id: GO:0008700
label: (R,S)-4-hydroxy-2-oxoglutarate aldolase activity
evidence_type: IDA
original_reference_id: PMID:21998747
qualifier: enables
review:
summary: Direct assay of recombinant human HOGA1 aldolase activity, including
crystal structure, catalytic-residue mutagenesis (Lys196, Tyr168), and kinetics.
action: ACCEPT
reason: This is the definitive experimental demonstration of HOGA1's core molecular
function. Recombinant human enzyme performs retro-aldol cleavage of HOG; catalytic
mutants (K196A, Y168F) abolish activity, establishing the mechanism. Core function.
supported_by:
- reference_id: PMID:21998747
supporting_text: The Y168F and K196A hHOGA variants exhibited no enzymatic activity
- reference_id: PMID:21998747
supporting_text: The activity of recombinant hHOGA proves that it is indeed
the aldolase identified in the genomic analysis of PH3 patients.
- term:
id: GO:0019470
label: trans-4-hydroxy-L-proline catabolic process
evidence_type: IDA
original_reference_id: PMID:21998747
qualifier: involved_in
review:
summary: HOGA1 catalyzes the terminal (final) step of the four-enzyme mitochondrial
hydroxyproline degradation pathway.
action: ACCEPT
reason: This is the core biological process for HOGA1. The enzyme catalyzes the
terminal step of 4-hydroxyproline catabolism, and UniProt describes its function
as catalyzing the final step in the metabolic pathway of hydroxyproline.
supported_by:
- reference_id: PMID:21998747
supporting_text: The degradation pathway for 4-Hyp (Figure 1) involves the step-wise
action of four mitochondrial enzymes
- reference_id: file:human/HOGA1/HOGA1-uniprot.txt
supporting_text: Catalyzes the final step in the metabolic pathway of
- term:
id: GO:0033609
label: oxalate metabolic process
evidence_type: IMP
original_reference_id: PMID:21896830
qualifier: involved_in
review:
summary: HOGA1 variants influence urinary oxalate; loss-of-function mutations
cause primary hyperoxaluria type 3, linking HOGA1 function to oxalate homeostasis.
action: KEEP_AS_NON_CORE
reason: The connection to oxalate metabolism is real but indirect - HOGA1 does
not act on oxalate directly; rather, its dysfunction perturbs glyoxylate/oxalate
handling and causes hyperoxaluria (PH3). This is a disease-level/physiological
link rather than the enzyme's direct catalytic role, so keep as non-core.
supported_by:
- reference_id: PMID:21896830
supporting_text: hypothesized to cause a gain of mitochondrial 4-hydroxy-2-oxoglutarate
aldolase
- reference_id: PMID:21896830
supporting_text: HOGA1 may be a predisposing factor for this
- term:
id: GO:0042803
label: protein homodimerization activity
evidence_type: IDA
original_reference_id: PMID:21998747
qualifier: enables
review:
summary: Structural study shows HOGA1 assembles via a "tight" dimer interface
into a homotetramer (dimer of dimers); the active site lies at the dimer interface.
action: ACCEPT
reason: The crystal structure directly demonstrates self-association. The biological
assembly is a homotetramer, but it is built as a dimer of dimers, and the active
site is formed at the tight dimer interface (a residue from the adjacent monomer,
Tyr140', contributes to the active site), so homodimerization is a genuine,
structurally-supported self-association activity. UniProt records the assembly
as a homotetramer.
supported_by:
- reference_id: PMID:21998747
supporting_text: reveal a tetrameric structure composed of a dimer of dimers
- reference_id: file:human/HOGA1/HOGA1-uniprot.txt
supporting_text: 'SUBUNIT: Homotetramer'
- term:
id: GO:0042866
label: pyruvate biosynthetic process
evidence_type: IDA
original_reference_id: PMID:21998747
qualifier: involved_in
review:
summary: Pyruvate is a co-product of the HOGA1-catalyzed cleavage of HOG (HOG
-> glyoxylate + pyruvate).
action: KEEP_AS_NON_CORE
reason: Pyruvate is genuinely produced by the HOGA1 reaction, so this annotation
is factually correct. However, pyruvate is a minor co-product of hydroxyproline
catabolism and HOGA1 is not a dedicated pyruvate-biosynthetic enzyme; keep as
a non-core annotation rather than a core function.
supported_by:
- reference_id: PMID:21998747
supporting_text: In the terminal reaction, HOG is cleaved by HOGA to produce
pyruvate and glyoxylate.
- term:
id: GO:0046487
label: glyoxylate metabolic process
evidence_type: IDA
original_reference_id: PMID:21998747
qualifier: involved_in
review:
summary: HOGA1 produces glyoxylate as a product of HOG cleavage, participating
in mitochondrial glyoxylate metabolism.
action: KEEP_AS_NON_CORE
reason: Correct - HOGA1 generates glyoxylate, so it participates in glyoxylate
metabolic process. This is a more accurate parent than "glyoxylate catabolic
process" (since HOGA1 makes, not degrades, glyoxylate), but it is a downstream/pathway
annotation rather than the core hydroxyproline-catabolic function; keep as non-core.
supported_by:
- reference_id: PMID:21998747
supporting_text: In the terminal reaction, HOG is cleaved by HOGA to produce
pyruvate and glyoxylate.
- term:
id: GO:0009436
label: glyoxylate catabolic process
evidence_type: IMP
original_reference_id: PMID:20797690
qualifier: involved_in
review:
summary: Mutations in HOGA1 (DHDPSL) cause primary hyperoxaluria type 3, establishing
HOGA1's role in the glyoxylate/hydroxyproline pathway by loss of function.
action: KEEP_AS_NON_CORE
reason: The disease-based IMP correctly places HOGA1 in the glyoxylate pathway,
but "glyoxylate catabolic process" is an imperfect descriptor since HOGA1 produces
rather than degrades glyoxylate; the core BP is hydroxyproline catabolism. Retain
as a non-core pathway-participation annotation.
supported_by:
- reference_id: PMID:20797690
supporting_text: cause a third type of PH (PH III)
- reference_id: PMID:20797690
supporting_text: the gene encoding 4-hydroxy-2-oxoglutarate
- term:
id: GO:0008700
label: (R,S)-4-hydroxy-2-oxoglutarate aldolase activity
evidence_type: ISS
original_reference_id: GO_REF:0000024
qualifier: enables
review:
summary: Sequence-similarity transfer of the core aldolase activity from the bovine
ortholog (Q0P5I5), which shares ~90% identity with human HOGA1.
action: ACCEPT
reason: Correct core molecular function, redundant with the direct experimental
(IDA) annotation to the same term. The bovine ortholog is 90.2% identical and
functionally characterized.
supported_by:
- reference_id: PMID:21998747
supporting_text: Sequence comparison of human HOGA with bovine HOGA (90.2% identity)
core_functions:
- description: Catalyzes the terminal step of the mitochondrial 4-hydroxyproline degradation
pathway, the retro-aldol cleavage of 4-hydroxy-2-oxoglutarate (HOG) into glyoxylate
and pyruvate, via a Schiff-base (type I aldolase) mechanism using Lys196 as the
catalytic nucleophile.
molecular_function:
id: GO:0008700
label: (R,S)-4-hydroxy-2-oxoglutarate aldolase activity
directly_involved_in:
- id: GO:0019470
label: trans-4-hydroxy-L-proline catabolic process
locations:
- id: GO:0005759
label: mitochondrial matrix
supported_by:
- reference_id: PMID:21998747
supporting_text: In the terminal reaction, HOG is cleaved by HOGA to produce pyruvate
and glyoxylate.
- reference_id: PMID:21998747
supporting_text: The Y168F and K196A hHOGA variants exhibited no enzymatic activity
- reference_id: file:human/HOGA1/HOGA1-uniprot.txt
supporting_text: Catalyzes the final step in the metabolic pathway of
proposed_new_terms: []
suggested_questions:
- question: Given that HOGA1 produces glyoxylate (an oxalate precursor), what is the
precise mechanism by which HOGA1 loss-of-function causes hyperoxaluria in PH3 -
accumulation of HOG or upstream intermediates, dominant-negative effects, or dysregulation
of glyoxylate detoxification?
suggested_experiments:
- description: Metabolomic quantification of HOG, glyoxylate, and oxalate in HOGA1-deficient
versus wild-type hepatocyte/renal models to test whether HOG accumulation (rather
than loss of glyoxylate production) drives the hyperoxaluric phenotype.
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:0000116
title: Automatic Gene Ontology annotation based on Rhea mapping
findings: []
- id: GO_REF:0000117
title: Electronic Gene Ontology annotations created by ARBA machine learning models
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:20797690
title: Mutations in DHDPSL are responsible for primary hyperoxaluria type III.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: PubMed-verified. Identifies DHDPSL/HOGA1 mutations as the cause of
primary hyperoxaluria type 3 and proposes HOGA1 as the gene encoding 4-hydroxy-2-oxoglutarate
aldolase.
- id: PMID:21896830
title: Primary hyperoxaluria type III gene HOGA1 (formerly DHDPSL) as a possible
risk factor for idiopathic calcium oxalate urolithiasis.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: PubMed-verified. Supports a loss-of-function mechanism for HOGA1
and links HOGA1 variants to oxalate/urolithiasis risk.
- id: PMID:21998747
title: 'Structural and biochemical studies of human 4-hydroxy-2-oxoglutarate aldolase:
implications for hydroxyproline metabolism in primary hyperoxaluria.'
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: PubMed-verified full text. Definitive structural and enzymatic characterization
of human HOGA1 - retro-aldol cleavage of HOG to pyruvate and glyoxylate, homotetramer
(dimer of dimers), catalytic residues Lys196/Tyr168, terminal step of hydroxyproline
degradation.
- id: PMID:27499296
title: Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory
Chain Function.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: High-throughput mitochondrial protein-interaction mapping; source
of a bare "protein binding" IPI (STARD7). Not informative for HOGA1's molecular
function.
- id: PMID:28514442
title: Architecture of the human interactome defines protein communities and disease
networks.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: Proteome-scale interactome (BioPlex); source of a bare "protein binding"
IPI (USP47). Not informative for molecular function.
- id: PMID:32296183
title: A reference map of the human binary protein interactome.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: Binary interactome map (HuRI); source of a bare "protein binding"
IPI (CIMAP1A). Not informative for molecular function.
- 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: Proteome-scale interactome (BioPlex 3.0); source of a bare "protein
binding" IPI (USP47). Not informative for molecular function.
- 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: High-confidence mitochondrial proteome; independent proteomic support
for mitochondrial localization of HOGA1.
- id: Reactome:R-HSA-6784423
title: HOGA1 tetramer aldol-cleaves 4-OH-2-oxoglutarate (HOG) to glyoxylate and
pyruvate
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: Reactome reaction curating the HOGA1-catalyzed HOG cleavage in the
mitochondrial matrix.
- id: file:human/HOGA1/HOGA1-uniprot.txt
title: UniProt entry Q86XE5 (HOGA1_HUMAN)
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: UniProt/Swiss-Prot record; source of function, subunit, subcellular
location, transit peptide, active-site, and disease annotations.