COQ2

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005743 mitochondrial inner membrane	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic (IBA) propagation of the inner-membrane location. This matches the experimentally established, multi-pass inner-membrane topology of COQ2 and its matrix-facing active site, so this is where the enzyme acts. Supporting Evidence: file:human/COQ2/COQ2-uniprot.txt Mitochondrion inner membrane
GO:0006744 ubiquinone biosynthetic process	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic (IBA) assignment of the core biological process. COQ2 orthologs across eukaryotes and bacteria (UbiA/Coq2) all carry out the 4-HB prenylation step of ubiquinone biosynthesis; this is the defining BP for the gene. Supporting Evidence: file:human/COQ2/COQ2-uniprot.txt Mediates the second step in the final reaction sequence of
GO:0008412 4-hydroxybenzoate polyprenyltransferase activity	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic (IBA) assignment of the defining molecular function. Consistent with the human enzyme's directly demonstrated PHB:polyprenyltransferase activity and the UbiA family assignment. Supporting Evidence: file:human/COQ2/COQ2-uniprot.txt Catalyzes the prenylation of para-
GO:0004659 prenyltransferase activity	IEA GO_REF:0000120	MODIFY	Summary: Correct but non-informative parent of the specific activity. The precise function GO:0008412 (4-hydroxybenzoate polyprenyltransferase activity) is already annotated and directly supported; this general term should be replaced by it. Proposed replacements: 4-hydroxybenzoate polyprenyltransferase activity
GO:0005743 mitochondrial inner membrane	IEA GO_REF:0000120	ACCEPT	Summary: Electronic (UniRule/SubCell) assignment of the inner-membrane location, redundant with the IDA and IBA annotations to the same term. Correct. Supporting Evidence: file:human/COQ2/COQ2-uniprot.txt Mitochondrion inner membrane
GO:0006744 ubiquinone biosynthetic process	IEA GO_REF:0000120	ACCEPT	Summary: Electronic (UniRule/UniPathway) assignment of the core BP, redundant with the experimental IDA/IMP and phylogenetic IBA annotations. Correct. Supporting Evidence: file:human/COQ2/COQ2-uniprot.txt Cofactor biosynthesis; ubiquinone biosynthesis.
GO:0008299 isoprenoid biosynthetic process	IEA GO_REF:0000104	MARK AS OVER ANNOTATED	Summary: Over-general and slightly misleading for the molecular event. COQ2 consumes a pre-formed all-trans polyprenyl diphosphate (the isoprenoid tail is synthesized by the mevalonate pathway and by decaprenyl-diphosphate synthase PDSS1/PDSS2); COQ2 itself condenses that tail onto 4-hydroxybenzoate rather than synthesizing an isoprenoid. The specific and accurate BP is ubiquinone biosynthetic process, which is already annotated. Keep only as a non-core electronic inference.
GO:0008412 4-hydroxybenzoate polyprenyltransferase activity	IEA GO_REF:0000120	ACCEPT	Summary: Electronic (UniRule; RHEA/EC:2.5.1.39) assignment of the defining molecular function, redundant with the experimental EXP/IMP and phylogenetic IBA/TAS annotations. Correct and core. Supporting Evidence: file:human/COQ2/COQ2-uniprot.txt 4-hydroxybenzoate polyprenyltransferase, mitochondrial
GO:0016020 membrane	IEA GO_REF:0000002	MODIFY	Summary: Correct but uninformatively general InterPro-based location. COQ2 is specifically an integral protein of the mitochondrial inner membrane, which is already annotated; replace with that specific term. Proposed replacements: mitochondrial inner membrane
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups	IEA GO_REF:0000002	MODIFY	Summary: Correct but very general InterPro-based grandparent of the specific activity. The precise 4-hydroxybenzoate polyprenyltransferase activity (GO:0008412) is already annotated and directly demonstrated; replace with that. Proposed replacements: 4-hydroxybenzoate polyprenyltransferase activity
GO:0006744 ubiquinone biosynthetic process	TAS Reactome:R-HSA-2142789	ACCEPT	Summary: Reactome traceable-author assignment of the core BP (Ubiquinol biosynthesis pathway). Correct and core. Supporting Evidence: file:human/COQ2/COQ2-uniprot.txt Cofactor biosynthesis; ubiquinone biosynthesis.
GO:0008412 4-hydroxybenzoate polyprenyltransferase activity	TAS Reactome:R-HSA-2162192	ACCEPT	Summary: Reactome traceable-author assignment of the defining molecular function, describing the reaction in which COQ2 ligates all-trans-decaprenyl diphosphate to 4-hydroxybenzoate to form 3-decaprenyl-4-hydroxybenzoate. Correct and core. Supporting Evidence: Reactome:R-HSA-2162192 4-Hydroxybenzoate polyprenyltransferase (COQ2) catalyses the combination of 4-hydroxybenzoic acid, aka para-hydroxybenzoic acid (PHB), with the polyisoprenoid tail all-trans-decaprenyl diphosphate (all-E-10PrP2) to form 3-decaprenyl-4-hydroxybenzoate (DHB)
GO:0008412 4-hydroxybenzoate polyprenyltransferase activity	EXP PMID:15153069 Isolation and functional expression of human COQ2, a gene en...	ACCEPT	Summary: Direct experimental support for the defining molecular function. Forsgren et al. cloned human COQ2, expressed it in a yeast coq2-null strain to restore CoQ biosynthesis, and showed formation of labelled CoQ from decaprenyl and nonaprenyl pyrophosphate precursors, demonstrating active PHB:polyprenyltransferase. Core. Supporting Evidence: PMID:15153069 CoQ formed when cells were incubated with labelled decaprenyl pyrophosphate and nonaprenyl pyrophosphate, showing that the human enzyme is active
GO:0005739 mitochondrion	HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an...	KEEP AS NON CORE	Summary: High-throughput mitochondrial proteome dataset localizes COQ2 to mitochondrion. Correct but coarse; the specific and experimentally supported location is the mitochondrial inner membrane, which is separately annotated. Keep as supporting, non-core localization evidence.
GO:0004659 prenyltransferase activity	IGI PMID:15153069 Isolation and functional expression of human COQ2, a gene en...	MARK AS OVER ANNOTATED	Summary: Genetic-interaction (complementation of a yeast coq2-null mutant) support for prenyltransferase activity. The evidence is experimental and valid, but the term is a non-informative parent of the specific 4-hydroxybenzoate polyprenyltransferase activity (GO:0008412) that is directly demonstrated in the same study. Retained as an over-annotation rather than removed (experimental evidence).
GO:0006744 ubiquinone biosynthetic process	IGI PMID:15153069 Isolation and functional expression of human COQ2, a gene en...	ACCEPT	Summary: Genetic-interaction support (human COQ2 rescues CoQ biosynthesis in a yeast coq2 null mutant) for involvement in ubiquinone biosynthesis. Correct and core; the involved_in annotations to the same term capture this more precisely. Supporting Evidence: PMID:15153069 rescued the growth of this yeast strain in the absence of a non-fermentable carbon source and restored CoQ biosynthesis
GO:0005743 mitochondrial inner membrane	IDA PMID:27493029 The COQ2 genotype predicts the severity of coenzyme Q10 defi...	ACCEPT	Summary: Direct experimental localization of COQ2 to the mitochondrial inner membrane, with defined topology (C-terminus facing the intermembrane space). This is the core, specific cellular component. Core. Supporting Evidence: PMID:27493029 its protein product localizes to mitochondria with the C-terminus facing the intermembrane space
GO:0006744 ubiquinone biosynthetic process	IMP PMID:16400613 A mutation in para-hydroxybenzoate-polyprenyl transferase (C...	ACCEPT	Summary: Mutant phenotype evidence: a homozygous COQ2 missense variant in patients caused a severe defect of CoQ10 biosynthesis (radioisotope assay in patient fibroblasts), establishing COQ2's requirement for ubiquinone biosynthesis. Core. Supporting Evidence: PMID:16400613 Radioisotope assays confirmed a severe defect of CoQ(10) biosynthesis in the fibroblasts of one patient
GO:0006744 ubiquinone biosynthetic process	IMP PMID:17374725 Missense mutation of the COQ2 gene causes defects of bioener...	ACCEPT	Summary: Mutant phenotype evidence: wild-type but not mutant COQ2 complements a COQ2-defective yeast strain, and COQ2 mutant patient fibroblasts have reduced polyprenyl-pHB transferase activity, confirming involvement in ubiquinone biosynthesis. Core. Supporting Evidence: PMID:17374725 human wild-type, but not mutant COQ2, functionally complements COQ2 defective yeast
GO:0006744 ubiquinone biosynthetic process	IMP PMID:27493029 The COQ2 genotype predicts the severity of coenzyme Q10 defi...	ACCEPT	Summary: Mutant phenotype evidence from a yeast complementation panel of all reported COQ2 alleles, where residual activity correlates with clinical severity of CoQ10 deficiency. Confirms COQ2 is required for ubiquinone biosynthesis. Core. Supporting Evidence: PMID:27493029 the residual activity of the mutant proteins correlates with the clinical phenotypes observed in patients
GO:0008412 4-hydroxybenzoate polyprenyltransferase activity	IMP PMID:16400613 A mutation in para-hydroxybenzoate-polyprenyl transferase (C...	ACCEPT	Summary: Mutant phenotype evidence for the defining molecular function: a COQ2 missense variant abolishes/severely reduces CoQ10 biosynthesis in patient fibroblasts, consistent with loss of PHB:polyprenyltransferase activity. Core. Supporting Evidence: PMID:16400613 the COQ2 gene, which encodes para-hydroxybenzoate-polyprenyl transferase
GO:0008412 4-hydroxybenzoate polyprenyltransferase activity	IMP PMID:17374725 Missense mutation of the COQ2 gene causes defects of bioener...	ACCEPT	Summary: Mutant phenotype evidence for the defining molecular function: polyprenyl-pHB transferase activity was reduced to 33-45% of controls in COQ2 mutant fibroblasts, directly linking the variant to loss of this activity. Core. Supporting Evidence: PMID:17374725 Polyprenyl-pHB transferase activity was 33-45% of controls in COQ2 mutant fibroblasts
GO:0005743 mitochondrial inner membrane	TAS Reactome:R-HSA-2162192	ACCEPT	Summary: Reactome traceable-author assignment of the inner-membrane location, redundant with the experimental IDA annotation to the same term. Correct. Supporting Evidence: file:human/COQ2/COQ2-uniprot.txt Mitochondrion inner membrane
GO:0006071 glycerol metabolic process	IGI PMID:15153069 Isolation and functional expression of human COQ2, a gene en...	MARK AS OVER ANNOTATED	Summary: Almost certainly a spurious legacy annotation. The IGI with/from is UniProtKB:P32378 (yeast GPD1, glycerol-3-phosphate dehydrogenase), and neither the cited COQ2 cloning paper nor any other evidence links COQ2 to glycerol metabolism; COQ2's demonstrated role is exclusively 4-HB prenylation in ubiquinone biosynthesis. Because this is an experimental (IGI) annotation it is flagged as over-annotated rather than removed, but it should not be treated as a real COQ2 function.
GO:0006744 ubiquinone biosynthetic process	IDA PMID:15153069 Isolation and functional expression of human COQ2, a gene en...	ACCEPT	Summary: Direct assay support for involvement in ubiquinone biosynthesis: expressed human COQ2 restored CoQ biosynthesis in a yeast coq2-null strain and produced labelled CoQ from polyprenyl pyrophosphate precursors. Core. Supporting Evidence: PMID:15153069 showing that the human enzyme is active and that it participates in the biosynthesis of CoQ

Gene Description

Existing Annotations Review

Core Functions

References

📚 Additional Documentation

Notes

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