Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0003955 NAD(P)H dehydrogenase (quinone) activity	IBA GO_REF:0000033	MODIFY	Summary: Phylogenetic (IBA) propagation of the family NAD(P)H:quinone oxidoreductase activity. This term (EC 1.6.5.2) specifies NAD(P)H as the electron donor, but NQO2 characteristically does not use NAD(P)H efficiently - it uses dihydronicotinamide riboside (NRH). The experimentally supported, cofactor-correct term is GO:0001512. Reason: NQO2 diverged from the NAD(P)H-using family archetype (NQO1) in electron-donor specificity. Replace the NAD(P)H term with the NRH-specific GO:0001512 (EC 1.10.5.1), which is already supported here by IDA and matches UniProt's EC and the RHEA:12364 reaction. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Proposed replacements: dihydronicotinamide riboside quinone reductase activity Supporting Evidence: PMID:10945627 its activity is normally latent, and a nonbiogenic co-substrate such as NRH [nicotinamide riboside (reduced)] is required for enzymatic activity file:human/NQO2/NQO2-hypotheses/function-hypothesis-go-0003955/openscientist.md recommend REMOVAL of the IBA GO:0003955
GO:0005829 cytosol	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic (IBA) annotation of cytosolic localization, consistent with UniProt (SUBCELLULAR LOCATION: Cytoplasm) and with direct experimental evidence for QR2 as a soluble cytosolic enzyme. Reason: Core localization. NQO2/QR2 is a well-established cytosolic enzyme; the IBA agrees with the IDA and TAS cytosol annotations.
GO:0001512 dihydronicotinamide riboside quinone reductase activity	IEA GO_REF:0000120	ACCEPT	Summary: Automated (IEA) annotation of the NRH:quinone reductase activity. This is the correct, cofactor-specific molecular function for NQO2 (EC 1.10.5.1; RHEA:12364), corroborated by IDA. Reason: Core catalytic function. Matches UniProt EC 1.10.5.1 and the demonstrated NRH-dependent quinone reduction; agrees with the IDA annotation of the same term.
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: Automated (IEA) cytoplasm annotation from UniProt subcellular-location mapping. Correct but a general parent of the more precise cytosol annotations. Reason: Consistent general localization; cytosol (GO:0005829) is the more informative core term.
GO:0005515 protein binding	IPI PMID:16189514 Towards a proteome-scale map of the human protein-protein in...	KEEP AS NON CORE	Summary: Generic protein binding from a large-scale (Y2H) human interactome mapping effort. Records a physical interaction but conveys no specific functional information. Reason: GO:0005515 is uninformative (project guideline: avoid protein binding) and derives from a high-throughput interactome screen; it does not inform NQO2's core enzymatic function.
GO:0005515 protein binding	IPI PMID:24606901 Cochaperone binding to LYR motifs confers specificity of iro...	KEEP AS NON CORE	Summary: Protein binding reported in a study of HSC20/HSCB cochaperone recognition of LYR motifs in iron-sulfur cluster delivery. Documents an interaction but is annotated only as generic protein binding. Reason: Uninformative as a molecular-function term; the interaction does not establish a core function for NQO2 and is not corroborated as a stable functional partnership.
GO:0005515 protein binding	IPI PMID:25416956 A proteome-scale map of the human interactome network.	KEEP AS NON CORE	Summary: Generic protein binding from a proteome-scale human interactome network map (systematic Y2H). Reason: High-throughput interactome hit; GO:0005515 is uninformative and non-core.
GO:0005515 protein binding	IPI PMID:31515488 Extensive disruption of protein interactions by genetic vari...	KEEP AS NON CORE	Summary: Generic protein binding from an interactome-perturbation study of genetic variants. Reason: High-throughput interactome hit; uninformative and non-core for NQO2 function.
GO:0005515 protein binding	IPI PMID:32296183 A reference map of the human binary protein interactome.	KEEP AS NON CORE	Summary: Generic protein binding from the HuRI reference map of the human binary protein interactome. Reason: High-throughput interactome hit; GO:0005515 is uninformative and non-core.
GO:0005829 cytosol	IDA GO_REF:0000052	ACCEPT	Summary: Direct (immunofluorescence-based) evidence for cytosolic localization of NQO2. Reason: Core localization, directly supported and consistent with all other cytosol annotations.
GO:1901662 quinone catabolic process	IDA PMID:18254726 Kinetic, thermodynamic and X-ray structural insights into th...	ACCEPT	Summary: Biological-process annotation for quinone catabolism/reduction. NQO2 reduces quinones to hydroquinones, feeding conjugation/detoxification, although QR2 can in some cases yield more reactive products than the parent quinone. Reason: Captures the principal biological role (quinone reduction/detoxification metabolism), the process context of the core catalytic activity. Supporting Evidence: PMID:18254726 it was believed that QR2 might also serve as a detoxification enzyme that can produce hydroquinones which are less toxic to cells compared with the parent quinones
GO:0016661 oxidoreductase activity, acting on other nitrogenous compounds as donors	IDA PMID:10945627 Bioactivation of 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB ...	MODIFY	Summary: General oxidoreductase term used for the NRH-dependent reductase activity. This term maps to EC 1.7.-.- (nitrogenous compounds as donors), a different EC branch than NQO2's EC 1.10.5.1; it mis-classifies the activity relative to the specific NRH:quinone reductase term. Reason: Replace with the specific, correctly-branched GO:0001512 (EC 1.10.5.1), which describes the demonstrated NRH:quinone reductase reaction and is already annotated here by IDA. Proposed replacements: dihydronicotinamide riboside quinone reductase activity
GO:0005829 cytosol	IDA PMID:10945627 Bioactivation of 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB ...	ACCEPT	Summary: Direct experimental evidence for cytosolic localization from the CB1954 bioactivation study. Reason: Core localization, directly supported.
GO:0009055 electron transfer activity	IDA PMID:10945627 Bioactivation of 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB ...	MARK AS OVER ANNOTATED	Summary: Electron transfer activity annotation. GO:0009055 denotes electron-carrier proteins operating within electron transport chains (cytochromes, ferredoxins, flavodoxins). NQO2 is a soluble cytosolic two-electron quinone reductase, not an electron-transport-chain carrier; its electron flow from NRH to quinone is already captured by its quinone reductase MF. Reason: The term implies an electron-carrier/ETC role that NQO2 does not have; the catalytic activity is better and fully represented by GO:0001512.
GO:0009055 electron transfer activity	IDA PMID:18254726 Kinetic, thermodynamic and X-ray structural insights into th...	MARK AS OVER ANNOTATED	Summary: Second electron transfer activity annotation (from the structural/kinetic paper). Same assessment as the PMID:10945627 annotation: GO:0009055 denotes electron-carrier proteins in electron transport chains, whereas NQO2 is a soluble cytosolic two-electron quinone reductase. Reason: NQO2 is not an electron-transport-chain carrier; its NRH-to-quinone electron flow is fully captured by the quinone reductase MF (GO:0001512).
GO:0016491 oxidoreductase activity	IDA PMID:10945627 Bioactivation of 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB ...	KEEP AS NON CORE	Summary: Root-level oxidoreductase activity. Correct but uninformatively general. Reason: Accurate parent term; the specific core MF is GO:0001512.
GO:0001512 dihydronicotinamide riboside quinone reductase activity	IDA PMID:18254726 Kinetic, thermodynamic and X-ray structural insights into th...	ACCEPT	Summary: Direct experimental annotation of the NRH:quinone reductase activity, the core catalytic function of NQO2 (EC 1.10.5.1; RHEA:12364). Structural/kinetic work characterized the QR2 active site and its dihydronicotinamide donor. Reason: Core molecular function, directly supported and matching UniProt EC and the Rhea reaction. Supporting Evidence: PMID:10945627 its activity is normally latent, and a nonbiogenic co-substrate such as NRH [nicotinamide riboside (reduced)] is required for enzymatic activity
GO:0008270 zinc ion binding	IDA PMID:18254726 Kinetic, thermodynamic and X-ray structural insights into th...	ACCEPT	Summary: Direct evidence for zinc binding. QR2 binds one structural Zn2+ per subunit (UniProt COFACTOR), resolved in the crystal structures. Reason: Bona fide structural cofactor of NQO2 (1 Zn2+/subunit), integral to the folded enzyme.
GO:0031404 chloride ion binding	IDA PMID:18254726 Kinetic, thermodynamic and X-ray structural insights into th...	KEEP AS NON CORE	Summary: Chloride ion binding observed in a QR2 crystal structure. Chloride is not listed among NQO2's functional cofactors (UniProt COFACTOR gives only FAD and Zn2+) and most likely reflects a crystallographic/buffer ion rather than a functional interaction. Reason: Real crystallographic observation but not a recognized functional cofactor; not part of the core function.
GO:0042803 protein homodimerization activity	IPI PMID:18254726 Kinetic, thermodynamic and X-ray structural insights into th...	ACCEPT	Summary: NQO2 is an obligate homodimer, with the active sites formed at the dimer interface; this is a specific, structurally-supported interaction (unlike generic protein binding). Reason: Genuine, informative homodimerization supported by crystal structures and confirmed as the biological unit (UniProt SUBUNIT: Homodimer). Non-core relative to catalysis but valid.
GO:0071949 FAD binding	IDA PMID:18254726 Kinetic, thermodynamic and X-ray structural insights into th...	ACCEPT	Summary: Direct evidence for FAD binding. NQO2 is a flavoprotein; each subunit binds FAD, the redox cofactor essential for the two-electron quinone reduction. Reason: Core cofactor binding; FAD is obligatory for catalysis and resolved in the QR2 structures.
GO:1904408 melatonin binding	IDA PMID:18254726 Kinetic, thermodynamic and X-ray structural insights into th...	KEEP AS NON CORE	Summary: Direct evidence that NQO2/QR2 binds melatonin - QR2 is the cytosolic "MT3" melatonin binding site. Melatonin is a competitive active-site inhibitor (vs the dihydronicotinamide donor), seen crystallographically in multiple active-site orientations. Reason: Well-evidenced and biologically notable (defining pharmacology of QR2/MT3), but it is inhibitor/ligand binding at the active site rather than the core catalytic function. Supporting Evidence: PMID:18254726 MT3 was purified to homogeneity and identified as QR2 (quinone reductase 2) PMID:18254726 melatonin binds in multiple orientations within the active sites of the QR2 dimer as opposed to an allosteric site
GO:1905594 resveratrol binding	IDA PMID:18254726 Kinetic, thermodynamic and X-ray structural insights into th...	KEEP AS NON CORE	Summary: Direct evidence for resveratrol binding. In the annotated paper the evidence is a biophysical binding assay - isothermal titration calorimetry (ITC) gave a Kd of ~39 nM - together with IC50 inhibition assays; resveratrol was used there as a positive-control active-site ligand. The QR2:resveratrol crystal structure itself is from an earlier study (Buryanovskyy et al. 2004, PDB 1SG0), which this paper reuses for molecular replacement and docking. Note the contrast with cao-1, where resveratrol is a substrate rather than an inhibitor. GO is obsoleting GO:1905594 resveratrol binding (go-ontology issues #32321/#32333, Jul 2026); NQO2 (P16083) is one of the two EXP-annotated proteins that triggered the obsoletion, the other being cao-1. Reason: Robustly evidenced inhibitor/ligand binding (ITC Kd ~39 nM), pharmacologically important, but not the core physiological catalytic function. The IDA to PMID:18254726 is supported by that paper's own ITC measurement; the primary structural evidence (PDB 1SG0) resides in Buryanovskyy et al. 2004 (Biochemistry; PMID:15350128), added to the references here. IMPORTANT distinction for the pending obsoletion: the obsoletion issue recommends reannotating both proteins "to enzyme activity with chebi id", but that fits only cao-1, where resveratrol is the catalytic SUBSTRATE (-> the new GO:7770086 resveratrol dioxygenase activity, go-ontology PR #32332 merged 2026-07-17). For NQO2 resveratrol is a competitive ACTIVE-SITE INHIBITOR, not a substrate or product, so there is no molecular-function replacement; on obsoletion this annotation should simply be dropped, not reannotated to a catalytic term. This is exactly the substrate-versus-inhibitor ambiguity that made GO:1905594 ill-defined. Supporting Evidence: PMID:18254726 Resveratrol was found to interact strongly with QR2 with a Kd of 39 nM
GO:0005829 cytosol	TAS Reactome:R-HSA-8936519	ACCEPT	Summary: Traceable-author-statement cytosol annotation from Reactome (NQO2:FAD dimer reduces quinones to hydroquinones). Reason: Consistent core localization; corroborates the IDA/IBA cytosol annotations.
GO:0070062 extracellular exosome	HDA PMID:23533145 In-depth proteomic analyses of exosomes isolated from expres...	KEEP AS NON CORE	Summary: High-throughput proteomic detection of NQO2 in exosomes (prostatic-secretion/urine exosome proteomics). Common for abundant cytosolic proteins; not evidence of a functional extracellular localization. Reason: Mass-spectrometry detection in an exosome preparation; NQO2 is fundamentally a cytosolic enzyme, so this is not a functionally informative localization.
GO:0070062 extracellular exosome	HDA PMID:19056867 Large-scale proteomics and phosphoproteomics of urinary exos...	KEEP AS NON CORE	Summary: High-throughput proteomic detection of NQO2 in urinary exosomes. Reason: Proteomics detection in exosomes; not a functional localization for this cytosolic enzyme.

Core Functions

FAD-dependent cytosolic quinone reductase that uses dihydronicotinamide riboside (NRH), not NAD(P)H, as the electron donor to catalyze two-electron reduction of quinones to hydroquinones (EC 1.10.5.1; RHEA:12364). Requires FAD and a structural Zn2+; functions as a homodimer.

Molecular Function:

dihydronicotinamide riboside quinone reductase activity

Directly Involved In:

quinone catabolic process

Cellular Locations:

cytosol

Supporting Evidence:

PMID:10945627
its activity is normally latent, and a nonbiogenic co-substrate such as NRH [nicotinamide riboside (reduced)] is required for enzymatic activity

References

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt

GO_REF:0000052

Gene Ontology annotation based on curation of immunofluorescence data

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:10945627

Bioactivation of 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB 1954) by human NAD(P)H quinone oxidoreductase 2: a novel co-substrate-mediated antitumor prodrug therapy.

NQO2 activity is latent unless supplied with a reduced dihydronicotinamide co-substrate such as NRH; NAD(P)H is not the physiological electron donor.

"its activity is normally latent, and a nonbiogenic co-substrate such as NRH [nicotinamide riboside (reduced)] is required for enzymatic activity"

PMID:16189514

Towards a proteome-scale map of the human protein-protein interaction network.

file:human/NQO2/NQO2-hypotheses/function-hypothesis-go-0003955/openscientist.md

OpenScientist blinded function-assignment report for NQO2 (NAD(P)H dehydrogenase (quinone) activity, GO:0003955)

An independent, blinded OpenScientist run neutrally tested whether NQO2 has NAD(P)H dehydrogenase (quinone) activity and concluded the term is over-annotated/substrate-incorrect because NQO2 uses NRH rather than NAD(P)H (NAD(P)H/EC 1.6.5.2 is the NQO1 activity), pointing to the already-annotated GO:0001512 - concurring with this review's MODIFY.

"recommend REMOVAL of the IBA GO:0003955"

PMID:15350128

Crystal structure of quinone reductase 2 in complex with resveratrol.

Resveratrol is a potent (Kd ~35 nM) inhibitor of QR2 that binds in the active-site cleft, with all three of its hydroxyl groups hydrogen-bonding to QR2 residues.

"resveratrol is a potent inhibitor of quinone reductase 2 (QR2) activity in vitro with a dissociation constant of 35 nM"
The resveratrol molecule is anchored in the QR2 active site via hydrogen bonds from all three of its hydroxyl groups.

"All three resveratrol hydroxyl groups form hydrogen bonds with amino acids from QR2"

PMID:18254726

Kinetic, thermodynamic and X-ray structural insights into the interaction of melatonin and analogues with quinone reductase 2.

QR2 is the cytosolic MT3 melatonin binding site; melatonin is a competitive active-site inhibitor seen in multiple orientations in the QR2 dimer.

"melatonin binds in multiple orientations within the active sites of the QR2 dimer as opposed to an allosteric site"
QR2 is a high-affinity (nanomolar) target of resveratrol, with a determined QR2:resveratrol crystal structure.

"It is one of the most potently inhibited (nanomolar) molecular targets of resveratrol, a natural polyphenol found in wine and peanuts, and the X-ray structure of QR2 in complex with resveratrol has been determined"

PMID:19056867

Large-scale proteomics and phosphoproteomics of urinary exosomes.

PMID:23533145

In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions in urine.

PMID:24606901

Cochaperone binding to LYR motifs confers specificity of iron sulfur cluster delivery.

PMID:25416956

A proteome-scale map of the human interactome network.

PMID:31515488

Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations.

PMID:32296183

A reference map of the human binary protein interactome.

Reactome:R-HSA-8936519

NQO2:FAD dimer reduces quinones to hydroquinones

Suggested Experiments

Experiment: Structure-guided separation-of-function mutants (active-site vs Zn/FAD sites) assayed for NRH: quinone reductase activity and for melatonin/resveratrol inhibition, to dissect the catalytic versus ligand-binding (MT3) roles of the active site.

Experiment: Metabolomic comparison of NQO2-proficient vs NQO2-null human cells challenged with model quinones, to determine which quinones are detoxified versus bioactivated and to test the NRH dependence in a cellular context.

Deep Research

OpenScientist

(NQO2-hypotheses/function-hypothesis-go-0003955/openscientist.md)

NQO2 (P16083) — Function-Assignment Hypothesis Review OpenScientist openscientist-autonomous 5 citations 4 artifacts 2026-07-18T13:51:02.026673 citations file

OpenScientist final report (text/html)

OpenScientist final report (application/pdf)

OpenScientist NQO2 GO decision table (application/json)

OpenScientist NQO2 GO decision table (image/png)

NQO2 (P16083) — Function-Assignment Hypothesis Review

Hypothesis: NQO2 has NAD(P)H dehydrogenase (quinone) activity (GO:0003955).
Focus: function_assignment · existing IBA annotation (GO_REF:0000033) · slug function-hypothesis-go-0003955
Gene: human NQO2 / UniProt P16083

Executive Judgment

Verdict: Over-annotated → recommend REMOVAL of the IBA GO:0003955 (activity real, but this specific term is substrate-incorrect and redundant).

NQO2 is unequivocally a flavin-dependent, two-electron quinone reductase, so the quinone-reductase concept is correct. But the specific term GO:0003955 "NAD(P)H dehydrogenase (quinone) activity" (reaction: NAD(P)H + quinone → NAD(P)⁺ + quinol) makes a cofactor/substrate claim that NQO2 does not satisfy. The definitive enzymology (Wu et al., 1997, PMID:9367528) shows NQO2 "uses dihydronicotinamide riboside (NRH) rather than NAD(P)H as an electron donor." UniProt (P16083) codifies this as EC 1.10.5.1; the NAD(P)H reaction (EC 1.6.5.2) belongs to the paralog NQO1 (P15559).

Two ontology facts (verified via QuickGO this iteration) make the recommendation removal rather than generalization:
1. The biochemically exact term GO:0001512 "dihydronicotinamide riboside quinone reductase activity" (NRH + quinone → nicotinamide riboside + hydroquinone) is already annotated to NQO2 with experimental evidence — IDA, PMID:18254726 (plus IEA GO_REF:0000120).
2. GO:0003955 is NOT an is_a ancestor of GO:0001512. They are siblings in different oxidoreductase subtrees, so GO:0003955 cannot be defended as a merely-less-specific but still-true parent. It is a distinct, incorrect molecular function.

The IBA is therefore a paralog over-annotation (GO:0003955 native to NQO1, propagated across the shared PANTHER family via GO_REF:0000033), and it is both wrong on substrate and redundant with the correct experimental term.

Most important caveat: Do not delete NQO2's reductase function from the model — it is captured accurately by GO:0001512. The action is limited to the mis-specified IBA row.

Evidence Matrix

Citation	Evidence type	Stance	Claim tested	Key finding	Context	Confidence / limitations
PMID:9367528 (Wu et al., 1997)	Direct assay (purified enzyme)	Refutes cofactor	Does NQO2 use NAD(P)H?	"NQO2 uses dihydronicotinamide riboside (NRH) rather than NAD(P)H as an electron donor"; FAD dimer; 2-e⁻ quinone reduction; dicoumarol-resistant	Recombinant human NQO2	High; definitive; in vitro
PMID:18254726 (Calamini et al., 2008)	Direct assay + X-ray structure	Supports correct term	NQO2 activity/structure & ligands	Kinetic/thermodynamic/X-ray characterization of QR2; source of NQO2 IDA GO:0001512, FAD binding, Zn²⁺ binding, melatonin binding	Human QR2 crystal	High
PMID:10945627 (Knox et al., 2000; context ref)	Direct assay	Qualifies (co-substrate)	NQO2 oxidoreductase mechanism	CB1954 bioactivation by NQO2 is co-substrate (NRH-analog)-mediated; IDA source for GO:0016491/0016661/0009055	Human NQO2	High; confirms NRH-type co-substrate, not NAD(P)H
UniProt P16083 (curated)	Database	Qualifies	Correct EC & reaction	EC 1.10.5.1; reaction NRH + quinone → nicotinamide riboside + quinol; cofactors FAD, Zn²⁺; 231 aa	Human	High
UniProt P15559 (NQO1)	Database (paralog)	Competing/explanatory	Which enzyme owns GO:0003955?	NQO1 = EC 1.6.5.2, NADH/NADPH reactions, 274 aa	Human	High; source of IBA carry-over
QuickGO ontology (this run)	Computational (ontology)	Qualifies	Is GO:0003955 a valid parent of the true term?	GO:0001512 is_a ancestors = GO:0016679→GO:0016491; GO:0003955 not an ancestor (sibling, not parent)	GO release	High; direct API result
QuickGO annotation (this run)	Database	Supports removal	Is the correct term already present?	NQO2 already has GO:0001512 (IDA, PMID:18254726; IEA); GO:0003955 present only as IBA (GO_REF:0000033)	UniProtKB:P16083	High
PMID:18996184 (Gaikwad et al., 2009)	Direct assay	Supports reductase core	Does NQO2 reduce quinones?	NQO2 reduces estrogen o-quinones using an NRH-type cofactor (BNAH); faster than NQO1	Human recombinant	Med-high
PMID:21506232 (Dufour et al., 2011)	Structural/inhibitor	Qualifies (flavoprotein)	Mechanism & FAD	FAD flavoprotein; inhibitors alkylate flavin; NQO1-distinct selectivity	X-ray + MS	High

GO Curation Implications

Lead (requires curator verification):

Molecular Function — REMOVE the IBA GO:0003955 from NQO2 (or mark NOT / do-not-propagate). It asserts NAD(P)H substrate that NQO2 cannot use and is a paralog carry-over from NQO1.
Retain the already-present GO:0001512 "dihydronicotinamide riboside quinone reductase activity" (IDA, PMID:18254726) as the accurate leaf MF term. No new term needs to be created.
Because GO:0003955 is a sibling (not ancestor) of GO:0001512, keeping it is not a harmless generalization — it introduces a false substrate assertion into the model.
Broader true ancestors already annotated (GO:0016491 oxidoreductase activity; GO:0016661 acting on other nitrogenous donors; GO:0009055 electron transfer activity; GO:0048038 quinone binding; GO:0071949 FAD binding; GO:0008270 zinc ion binding) remain valid. Avoid defaulting to generic "protein binding."

GO decision table

Term	Current on NQO2	Recommended action	Basis
GO:0003955 NAD(P)H dehydrogenase (quinone) activity	IBA (GO_REF:0000033)	Remove / NOT — substrate-incorrect, paralog carry-over, non-ancestral to true term	PMID:9367528; UniProt EC 1.10.5.1; QuickGO ancestry
GO:0001512 dihydronicotinamide riboside quinone reductase activity	IDA (PMID:18254726) + IEA	Retain as accurate MF leaf term	PMID:9367528, 18254726; EC 1.10.5.1

{{figure:NQO2_GO_decision_table.png|caption=GO molecular-function decision table for NQO2 (P16083). GO:0003955 "NAD(P)H dehydrogenase (quinone) activity" (IBA, GO_REF:0000033) is substrate-incorrect (NQO2 uses NRH, not NAD(P)H; PMID:9367528) and redundant with the already-annotated, experimentally-supported GO:0001512 "dihydronicotinamide riboside quinone reductase activity" (IDA, PMID:18254726). Recommended action: remove GO:0003955; retain GO:0001512.}}

Mechanistic Scope

Immediate molecular function tested: FAD-mediated two-electron reduction of quinones to hydroquinones, electrons supplied by a dihydronicotinamide riboside (NRH) donor in a ping-pong mechanism; Zn²⁺ is structural.
Correctly in scope: quinone reduction (menadione and other quinones, estrogen o-quinones, vitamin K quinones), NRH-dependent nitroreduction (CB1954). Captured by GO:0001512.
Out of scope for this MF term (BP/CC or ligand-binding): neuronal "memory constraint"/metabolic-buffer role (Rosenblum lab), Alzheimer's phenotype modulation, melatonin MT3 binding-site identity (GO:1904408) and resveratrol binding (GO:1905594). These are downstream physiology or ligand properties, not the electron-donor chemistry adjudicated here.

Conflicts and Alternatives

Paralog confusion (primary): GO:0003955 is correct for NQO1 (EC 1.6.5.2, NADH/NADPH). Its presence on NQO2 is explained by IBA propagation, not NQO2 biochemistry. Structural basis: NQO2 (231 aa) lacks the ~43-residue C-terminal region present in NQO1 (274 aa) that helps form the adenosine/2′-phosphate NAD(P)H-binding site, so NQO2 uses the smaller NRH.
In-vitro cofactor surrogates: NQO2 assays use synthetic donors (BNAH; EP-0152R) because free NRH is not a standard bulk metabolite; consistent with EC 1.10.5.1, not with NAD(P)H use.
No credible primary report shows efficient NAD(P)H-driven catalysis by NQO2.
Self-correction: Iteration 1 tentatively named the replacement term GO:0033856; that ID is actually pyridoxine 5′-phosphate synthase activity. The correct term is GO:0001512, confirmed via QuickGO.

Knowledge Gaps

Physiological NRH source in vivo. Checked: literature uses in-vitro NRH/BNAH surrogates. Matters for BP context, not the MF term. Resolve via tissue metabolomics for NRH and NRH-generating enzymes.
Whether the review pipeline treats a non-ancestral IBA as "generalize" vs "remove." Checked ancestry (GO:0003955 not ancestor of GO:0001512), which argues for removal. Curator should confirm project policy.
Quantitative NAD(P)H vs NRH kinetics. Existing data are qualitative (NRH-preference). A kcat/Km ratio would formally bound the error; confirmatory only.

Discriminating Tests

Side-by-side kinetics: NQO2 quinone reduction with NRH/BNAH vs NADH vs NADPH → expect robust NRH activity, negligible NAD(P)H (discriminates GO:0001512 from GO:0003955).
Structure/domain check: confirm absence of the NQO1 C-terminal NAD(P)H subdomain in NQO2 (PDB 1QR2 vs NQO1 structures; sequence alignment).
Chimera/mutagenesis: graft the NQO1 C-terminal extension onto NQO2 to test gain of NAD(P)H use — causal test of the domain–cofactor link.

Curation Leads (require curator verification)

Candidate action: Remove/NOT the IBA GO:0003955 on NQO2; retain existing IDA GO:0001512.
Candidate reference to verify (donor specificity): PMID:9367528 — "NQO2 uses dihydronicotinamide riboside (NRH) rather than NAD(P)H as an electron donor. It catalyzes a two-electron reduction of quinones and oxidation-reduction dyes."
Candidate reference supporting the correct term (already the IDA source): PMID:18254726 (Calamini et al., 2008, QR2 kinetics + X-ray) — verify it is the IDA basis for GO:0001512.
Context reference: PMID:10945627 (CB1954 co-substrate-mediated bioactivation) confirms NRH-type co-substrate, not NAD(P)H.
Database support: UniProt P16083 (EC 1.10.5.1, NRH→quinol reaction, FAD+Zn²⁺); QuickGO ancestry showing GO:0003955 is not an ancestor of GO:0001512.
Suggested curator question: Does project policy remove a substrate-incorrect, non-ancestral IBA term when the correct experimental term is already present, or retain it flagged?
Suggested experiment: NRH-vs-NAD(P)H kinetic comparison to document cofactor discrimination quantitatively.

Provenance (executed this review)

UniProt REST: NQO2 P16083 = 231 aa, EC 1.10.5.1, NRH→quinol, FAD+Zn²⁺; NQO1 P15559 = 274 aa, EC 1.6.5.2, NAD(H)/NADP(H). Confirms paralog cofactor divergence + 43-aa length difference.
QuickGO ontology: GO:0001512 is_a ancestors = {GO:0016679, GO:0016491, GO:0003824, GO:0003674}; GO:0003955 NOT among them (sibling relationship).
QuickGO annotation (UniProtKB:P16083, MF): GO:0001512 = IDA (PMID:18254726) + IEA; GO:0003955 = IBA only (GO_REF:0000033).
NCBI eSummary: PMID:18254726 = QR2 melatonin kinetics/X-ray; PMID:10945627 = CB1954 co-substrate bioactivation.
Sequence comparison (UniProt FASTA, computed): NQO2 231 aa vs NQO1 274 aa; NQO1 carries exactly 43 extra C-terminal residues (…NFQAGFLMKKEVQDEEKNKKFGLSVGHHLGKSIPTDNQIKARK) absent in NQO2 — the C-terminal segment forming part of the NAD(P)H adenosine-binding site, i.e. the structural reason NQO2 cannot use NAD(P)H.
Literature: PMID:9367528 (definitive), 18996184, 21506232, plus review 18374191.

Artifacts generated

NQO2_GO_decision_table.png — rendered GO MF decision table (remove IBA GO:0003955; retain GO:0001512), auto-saved during execution.
Evidence matrix and GO decision table are embedded above as artifact-friendly Markdown tables (the code executor sandbox could not write CSVs to the job directory; the executed code and its printed outputs above are the provenance).

Artifacts

📚 Additional Documentation

Notes

(NQO2-notes.md)

NQO2 (P16083, NQO2_HUMAN) — review notes

Gene identity and core function

NQO2 = NRH:quinone oxidoreductase 2 / quinone reductase 2 (QR2); UniProt recommended name
Ribosyldihydronicotinamide dehydrogenase [quinone], EC 1.10.5.1. A 231-aa cytosolic FAD
flavoprotein, homodimer, member of the NAD(P)H:quinone oxidoreductase family (paralog of NQO1).

Defining biochemical distinction from NQO1: NQO2 does not use NAD(P)H efficiently as the
electron donor. Instead it uses dihydronicotinamide riboside (NRH) (and other reduced
N-ribosyl/N-alkyl dihydronicotinamides) as the reducing co-substrate.
PMID:10945627
UniProt MISCELLANEOUS: "Uses dihydronicotinamide riboside (NRH) rather than NAD(P)H as an electron donor."

Catalysis: two-electron reduction of quinones to hydroquinones (quinols), NRH + quinone + H+ →
N-ribosylnicotinamide + quinol (RHEA:12364; EC 1.10.5.1; GO:0001512). FAD-dependent.
Cofactors: FAD (flavin) and one structural Zn2+ per subunit (UniProt COFACTOR).
Biological role: quinone reduction/detoxification (produces less-toxic hydroquinones for
conjugation), though notably QR2 can in some cases generate more reactive species than the
parent quinone PMID:18254726. Also implicated in prodrug bioactivation (CB1954, mitomycin C).

Pharmacology — the MT3 melatonin site and resveratrol

QR2 is the long-sought cytosolic "MT3" melatonin binding site.
PMID:18254726
Melatonin is a competitive inhibitor of QR2 (vs the dihydronicotinamide donor), binding in the
active site (not allosteric): PMID:18254726 and X-ray structures show
PMID:18254726.

QR2 is also one of the highest-affinity molecular targets of resveratrol (an inhibitor here,
in contrast to cao-1 where resveratrol is a substrate):
PMID:18254726.

So the melatonin binding and resveratrol binding IDA annotations reflect inhibitor/ligand
binding at the active site, well-evidenced (co-crystals, ITC/kinetics) but pharmacological rather
than the core catalytic function → KEEP_AS_NON_CORE.

Provenance of the resveratrol binding IDA (GO:1905594 → PMID:18254726): In the annotated
paper the direct evidence is a binding assay, not a structure — ITC gave a Kd of ~39 nM
PMID:18254726, plus IC50
inhibition assays; resveratrol served as a positive control there. The crystal structure of the
QR2:resveratrol complex is from an earlier paper — Buryanovskyy et al. 2004 (PDB 1SG0; PMID:15350128),
who also first measured the Kd (~35 nM) by intrinsic tryptophan fluorescence — which Calamini et al.
reuse for molecular replacement/docking. Buryanovskyy 2004 is a candidate reference to add (it is the
primary structural + first-binding source but is absent from NQO2's GOA reference set).

Annotation review decisions (26 GOA annotations)

Molecular function — catalytic

GO:0001512 dihydronicotinamide riboside quinone reductase activity (IDA PMID:18254726; IEA) →
ACCEPT (core). Exactly matches EC 1.10.5.1 / RHEA:12364.
GO:0003955 NAD(P)H dehydrogenase (quinone) activity (IBA) → MODIFY → GO:0001512. This term
maps to EC 1.6.5.2 (NAD(P)H donor); NQO2 uses NRH, not NAD(P)H. Family IBA propagated the
NQO1-type activity. Replace with the NRH-specific term.
GO:0016661 oxidoreductase activity, acting on other nitrogenous compounds as donors (IDA
PMID:10945627) → MODIFY → GO:0001512. Maps to EC 1.7.-.- (nitrogenous donors), a different
branch than NQO2's EC 1.10.5.1; the specific NRH:quinone reductase term is the correct classification.
GO:0016491 oxidoreductase activity (IDA PMID:10945627) → KEEP_AS_NON_CORE. Correct root
term but uninformatively general.
GO:0009055 electron transfer activity (IDA PMID:10945627, PMID:18254726) → MARK_AS_OVER_ANNOTATED.
This term denotes electron-carrier proteins in electron transport chains; QR2 is a soluble
two-electron quinone reductase, and its electron flow is already captured by the quinone reductase MF.

Molecular function — cofactor/ligand binding

GO:0071949 FAD binding (IDA) → ACCEPT (core cofactor; flavoprotein).
GO:0008270 zinc ion binding (IDA) → ACCEPT (structural Zn2+, 1/subunit per UniProt).
GO:0031404 chloride ion binding (IDA) → KEEP_AS_NON_CORE. Not a recognized functional
cofactor (absent from UniProt COFACTOR); likely a crystallographic ion.
GO:1904408 melatonin binding (IDA) → KEEP_AS_NON_CORE (MT3 site; active-site competitive inhibitor).
GO:1905594 resveratrol binding (IDA) → KEEP_AS_NON_CORE (nanomolar inhibitor binding).
GO:0042803 protein homodimerization activity (IPI PMID:18254726) → ACCEPT (genuine homodimer;
informative, unlike bare protein binding). Non-core.

Molecular function — protein binding (5× IPI, GO:0005515)

PMID:16189514, 25416956, 31515488, 32296183 = large-scale interactome (Y2H) screens;
PMID:24606901 = HSCB/HSC20 LYR-motif cochaperone study. All → KEEP_AS_NON_CORE. protein binding
is uninformative (project guideline: avoid); none identifies a functional partnership that revises
the core-function picture.

Biological process

GO:1901662 quinone catabolic process (IDA PMID:18254726) → ACCEPT. Captures the quinone
reduction/detoxification role (main BP).

Cellular component

GO:0005829 cytosol (IDA GO_REF:0000052; also TAS Reactome, IBA, IDA PMID:10945627) → ACCEPT (core).
QR2 is cytosolic.
GO:0005737 cytoplasm (IEA) → ACCEPT (general parent).
GO:0070062 extracellular exosome (HDA PMID:23533145, PMID:19056867) → KEEP_AS_NON_CORE.
High-throughput exosome proteomics detection; not a functionally informative localization for a
cytosolic enzyme.

Enzyme-function / Rhea comparison

Core MF GO:0001512 carries EC=1.10.5.1, RHEA:12364, MetaCyc 1.10.99.2-RXN, Reactome R-HSA-8936519 —
a fully-resolved, reaction-specific term (unlike cao-1, where no reaction-level term existed).
The IBA GO:0003955 carries EC=1.6.5.2 (NAD(P)H) — the wrong cofactor branch for NQO2; this is the
crux of the MODIFY.
Contrast with cao-1: there resveratrol is the substrate of a stilbenoid dioxygenase; here
resveratrol is a high-affinity inhibitor of a quinone reductase — same molecule, opposite role,
and a good illustration of why resveratrol binding alone (causal-role, ligand-agnostic) underspecifies biology.

📄 View Raw YAML

id: P16083
gene_symbol: NQO2
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  NQO2 (NRH:quinone oxidoreductase 2 / quinone reductase 2, QR2; UniProt recommended name
  ribosyldihydronicotinamide dehydrogenase [quinone], EC 1.10.5.1) is a cytosolic FAD-dependent
  flavoprotein of the NAD(P)H:quinone oxidoreductase family and a paralog of NQO1. It functions
  as a homodimer, with each subunit binding one FAD and one structural zinc ion. NQO2 catalyzes
  the two-electron reduction of quinones to hydroquinones (quinols), a reaction linked to quinone
  detoxification and to the metabolism/bioactivation of quinone-derived and nitroaromatic
  compounds (e.g. the prodrug CB1954). Its defining biochemical feature, distinguishing it from
  NQO1, is that it does not use NAD(P)H efficiently; instead it requires dihydronicotinamide
  riboside (NRH) or other reduced N-ribosyl/N-alkyl dihydronicotinamides as the electron donor.
  NQO2 is also the cytosolic "MT3" melatonin binding site: melatonin and the polyphenol resveratrol
  are high-affinity active-site inhibitors, making QR2 a notable pharmacological target.
existing_annotations:
- term:
    id: GO:0003955
    label: NAD(P)H dehydrogenase (quinone) activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      Phylogenetic (IBA) propagation of the family NAD(P)H:quinone oxidoreductase activity. This
      term (EC 1.6.5.2) specifies NAD(P)H as the electron donor, but NQO2 characteristically does
      not use NAD(P)H efficiently - it uses dihydronicotinamide riboside (NRH). The
      experimentally supported, cofactor-correct term is GO:0001512.
    action: MODIFY
    reason: >-
      NQO2 diverged from the NAD(P)H-using family archetype (NQO1) in electron-donor specificity.
      Replace the NAD(P)H term with the NRH-specific GO:0001512 (EC 1.10.5.1), which is already
      supported here by IDA and matches UniProt's EC and the RHEA:12364 reaction.
    proposed_replacement_terms:
      - id: GO:0001512
        label: dihydronicotinamide riboside quinone reductase activity
    propagation_review:
      root_cause: PROPAGATION_BAD
      failure_modes:
        - FUNCTIONAL_DIVERGENCE
    supported_by:
      - reference_id: PMID:10945627
        supporting_text: >-
          its activity is normally latent, and a nonbiogenic co-substrate such as NRH [nicotinamide
          riboside (reduced)] is required for enzymatic activity
      - reference_id: file:human/NQO2/NQO2-hypotheses/function-hypothesis-go-0003955/openscientist.md
        supporting_text: >-
          recommend REMOVAL of the IBA GO:0003955
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      Phylogenetic (IBA) annotation of cytosolic localization, consistent with UniProt
      (SUBCELLULAR LOCATION: Cytoplasm) and with direct experimental evidence for QR2 as a soluble
      cytosolic enzyme.
    action: ACCEPT
    reason: >-
      Core localization. NQO2/QR2 is a well-established cytosolic enzyme; the IBA agrees with the
      IDA and TAS cytosol annotations.
- term:
    id: GO:0001512
    label: dihydronicotinamide riboside quinone reductase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      Automated (IEA) annotation of the NRH:quinone reductase activity. This is the correct,
      cofactor-specific molecular function for NQO2 (EC 1.10.5.1; RHEA:12364), corroborated by IDA.
    action: ACCEPT
    reason: >-
      Core catalytic function. Matches UniProt EC 1.10.5.1 and the demonstrated NRH-dependent
      quinone reduction; agrees with the IDA annotation of the same term.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: >-
      Automated (IEA) cytoplasm annotation from UniProt subcellular-location mapping. Correct but
      a general parent of the more precise cytosol annotations.
    action: ACCEPT
    reason: >-
      Consistent general localization; cytosol (GO:0005829) is the more informative core term.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16189514
  qualifier: enables
  review:
    summary: >-
      Generic protein binding from a large-scale (Y2H) human interactome mapping effort. Records a
      physical interaction but conveys no specific functional information.
    action: KEEP_AS_NON_CORE
    reason: >-
      GO:0005515 is uninformative (project guideline: avoid protein binding) and derives from a
      high-throughput interactome screen; it does not inform NQO2's core enzymatic function.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:24606901
  qualifier: enables
  review:
    summary: >-
      Protein binding reported in a study of HSC20/HSCB cochaperone recognition of LYR motifs in
      iron-sulfur cluster delivery. Documents an interaction but is annotated only as generic
      protein binding.
    action: KEEP_AS_NON_CORE
    reason: >-
      Uninformative as a molecular-function term; the interaction does not establish a core
      function for NQO2 and is not corroborated as a stable functional partnership.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25416956
  qualifier: enables
  review:
    summary: >-
      Generic protein binding from a proteome-scale human interactome network map (systematic Y2H).
    action: KEEP_AS_NON_CORE
    reason: >-
      High-throughput interactome hit; GO:0005515 is uninformative and non-core.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:31515488
  qualifier: enables
  review:
    summary: >-
      Generic protein binding from an interactome-perturbation study of genetic variants.
    action: KEEP_AS_NON_CORE
    reason: >-
      High-throughput interactome hit; uninformative and non-core for NQO2 function.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  qualifier: enables
  review:
    summary: >-
      Generic protein binding from the HuRI reference map of the human binary protein interactome.
    action: KEEP_AS_NON_CORE
    reason: >-
      High-throughput interactome hit; GO:0005515 is uninformative and non-core.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  qualifier: located_in
  review:
    summary: >-
      Direct (immunofluorescence-based) evidence for cytosolic localization of NQO2.
    action: ACCEPT
    reason: >-
      Core localization, directly supported and consistent with all other cytosol annotations.
- term:
    id: GO:1901662
    label: quinone catabolic process
  evidence_type: IDA
  original_reference_id: PMID:18254726
  qualifier: involved_in
  review:
    summary: >-
      Biological-process annotation for quinone catabolism/reduction. NQO2 reduces quinones to
      hydroquinones, feeding conjugation/detoxification, although QR2 can in some cases yield more
      reactive products than the parent quinone.
    action: ACCEPT
    reason: >-
      Captures the principal biological role (quinone reduction/detoxification metabolism), the
      process context of the core catalytic activity.
    supported_by:
      - reference_id: PMID:18254726
        supporting_text: >-
          it was believed that QR2 might also serve as a detoxification enzyme that can produce
          hydroquinones which are less toxic to cells compared with the parent quinones
- term:
    id: GO:0016661
    label: oxidoreductase activity, acting on other nitrogenous compounds as donors
  evidence_type: IDA
  original_reference_id: PMID:10945627
  qualifier: enables
  review:
    summary: >-
      General oxidoreductase term used for the NRH-dependent reductase activity. This term maps to
      EC 1.7.-.- (nitrogenous compounds as donors), a different EC branch than NQO2's EC 1.10.5.1;
      it mis-classifies the activity relative to the specific NRH:quinone reductase term.
    action: MODIFY
    reason: >-
      Replace with the specific, correctly-branched GO:0001512 (EC 1.10.5.1), which describes the
      demonstrated NRH:quinone reductase reaction and is already annotated here by IDA.
    proposed_replacement_terms:
      - id: GO:0001512
        label: dihydronicotinamide riboside quinone reductase activity
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IDA
  original_reference_id: PMID:10945627
  qualifier: located_in
  review:
    summary: >-
      Direct experimental evidence for cytosolic localization from the CB1954 bioactivation study.
    action: ACCEPT
    reason: >-
      Core localization, directly supported.
- term:
    id: GO:0009055
    label: electron transfer activity
  evidence_type: IDA
  original_reference_id: PMID:10945627
  qualifier: enables
  review:
    summary: >-
      Electron transfer activity annotation. GO:0009055 denotes electron-carrier proteins operating
      within electron transport chains (cytochromes, ferredoxins, flavodoxins). NQO2 is a soluble
      cytosolic two-electron quinone reductase, not an electron-transport-chain carrier; its
      electron flow from NRH to quinone is already captured by its quinone reductase MF.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The term implies an electron-carrier/ETC role that NQO2 does not have; the catalytic activity
      is better and fully represented by GO:0001512.
- term:
    id: GO:0009055
    label: electron transfer activity
  evidence_type: IDA
  original_reference_id: PMID:18254726
  qualifier: enables
  review:
    summary: >-
      Second electron transfer activity annotation (from the structural/kinetic paper). Same
      assessment as the PMID:10945627 annotation: GO:0009055 denotes electron-carrier proteins in
      electron transport chains, whereas NQO2 is a soluble cytosolic two-electron quinone reductase.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      NQO2 is not an electron-transport-chain carrier; its NRH-to-quinone electron flow is fully
      captured by the quinone reductase MF (GO:0001512).
- term:
    id: GO:0016491
    label: oxidoreductase activity
  evidence_type: IDA
  original_reference_id: PMID:10945627
  qualifier: enables
  review:
    summary: >-
      Root-level oxidoreductase activity. Correct but uninformatively general.
    action: KEEP_AS_NON_CORE
    reason: >-
      Accurate parent term; the specific core MF is GO:0001512.
- term:
    id: GO:0001512
    label: dihydronicotinamide riboside quinone reductase activity
  evidence_type: IDA
  original_reference_id: PMID:18254726
  qualifier: enables
  review:
    summary: >-
      Direct experimental annotation of the NRH:quinone reductase activity, the core catalytic
      function of NQO2 (EC 1.10.5.1; RHEA:12364). Structural/kinetic work characterized the QR2
      active site and its dihydronicotinamide donor.
    action: ACCEPT
    reason: >-
      Core molecular function, directly supported and matching UniProt EC and the Rhea reaction.
    supported_by:
      - reference_id: PMID:10945627
        supporting_text: >-
          its activity is normally latent, and a nonbiogenic co-substrate such as NRH [nicotinamide
          riboside (reduced)] is required for enzymatic activity
- term:
    id: GO:0008270
    label: zinc ion binding
  evidence_type: IDA
  original_reference_id: PMID:18254726
  qualifier: enables
  review:
    summary: >-
      Direct evidence for zinc binding. QR2 binds one structural Zn2+ per subunit (UniProt COFACTOR),
      resolved in the crystal structures.
    action: ACCEPT
    reason: >-
      Bona fide structural cofactor of NQO2 (1 Zn2+/subunit), integral to the folded enzyme.
- term:
    id: GO:0031404
    label: chloride ion binding
  evidence_type: IDA
  original_reference_id: PMID:18254726
  qualifier: enables
  review:
    summary: >-
      Chloride ion binding observed in a QR2 crystal structure. Chloride is not listed among NQO2's
      functional cofactors (UniProt COFACTOR gives only FAD and Zn2+) and most likely reflects a
      crystallographic/buffer ion rather than a functional interaction.
    action: KEEP_AS_NON_CORE
    reason: >-
      Real crystallographic observation but not a recognized functional cofactor; not part of the
      core function.
- term:
    id: GO:0042803
    label: protein homodimerization activity
  evidence_type: IPI
  original_reference_id: PMID:18254726
  qualifier: enables
  review:
    summary: >-
      NQO2 is an obligate homodimer, with the active sites formed at the dimer interface; this is a
      specific, structurally-supported interaction (unlike generic protein binding).
    action: ACCEPT
    reason: >-
      Genuine, informative homodimerization supported by crystal structures and confirmed as the
      biological unit (UniProt SUBUNIT: Homodimer). Non-core relative to catalysis but valid.
- term:
    id: GO:0071949
    label: FAD binding
  evidence_type: IDA
  original_reference_id: PMID:18254726
  qualifier: enables
  review:
    summary: >-
      Direct evidence for FAD binding. NQO2 is a flavoprotein; each subunit binds FAD, the redox
      cofactor essential for the two-electron quinone reduction.
    action: ACCEPT
    reason: >-
      Core cofactor binding; FAD is obligatory for catalysis and resolved in the QR2 structures.
- term:
    id: GO:1904408
    label: melatonin binding
  evidence_type: IDA
  original_reference_id: PMID:18254726
  qualifier: enables
  review:
    summary: >-
      Direct evidence that NQO2/QR2 binds melatonin - QR2 is the cytosolic "MT3" melatonin binding
      site. Melatonin is a competitive active-site inhibitor (vs the dihydronicotinamide donor),
      seen crystallographically in multiple active-site orientations.
    action: KEEP_AS_NON_CORE
    reason: >-
      Well-evidenced and biologically notable (defining pharmacology of QR2/MT3), but it is
      inhibitor/ligand binding at the active site rather than the core catalytic function.
    supported_by:
      - reference_id: PMID:18254726
        supporting_text: >-
          MT3 was purified to homogeneity and identified as QR2 (quinone reductase 2)
      - reference_id: PMID:18254726
        supporting_text: >-
          melatonin binds in multiple orientations within the active sites of the QR2 dimer as
          opposed to an allosteric site
- term:
    id: GO:1905594
    label: resveratrol binding
  evidence_type: IDA
  original_reference_id: PMID:18254726
  qualifier: enables
  review:
    summary: >-
      Direct evidence for resveratrol binding. In the annotated paper the evidence is a biophysical
      binding assay - isothermal titration calorimetry (ITC) gave a Kd of ~39 nM - together with
      IC50 inhibition assays; resveratrol was used there as a positive-control active-site ligand.
      The QR2:resveratrol crystal structure itself is from an earlier study (Buryanovskyy et al.
      2004, PDB 1SG0), which this paper reuses for molecular replacement and docking. Note the
      contrast with cao-1, where resveratrol is a substrate rather than an inhibitor. GO is obsoleting
      GO:1905594 resveratrol binding (go-ontology issues #32321/#32333, Jul 2026); NQO2 (P16083) is
      one of the two EXP-annotated proteins that triggered the obsoletion, the other being cao-1.
    action: KEEP_AS_NON_CORE
    reason: >-
      Robustly evidenced inhibitor/ligand binding (ITC Kd ~39 nM), pharmacologically important, but
      not the core physiological catalytic function. The IDA to PMID:18254726 is supported by that
      paper's own ITC measurement; the primary structural evidence (PDB 1SG0) resides in Buryanovskyy
      et al. 2004 (Biochemistry; PMID:15350128), added to the references here. IMPORTANT distinction
      for the pending obsoletion: the obsoletion issue recommends reannotating both proteins "to enzyme
      activity with chebi id", but that fits only cao-1, where resveratrol is the catalytic SUBSTRATE
      (-> the new GO:7770086 resveratrol dioxygenase activity, go-ontology PR #32332 merged
      2026-07-17). For NQO2 resveratrol is a competitive
      ACTIVE-SITE INHIBITOR, not a substrate or product, so there is no molecular-function replacement;
      on obsoletion this annotation should simply be dropped, not reannotated to a catalytic term. This
      is exactly the substrate-versus-inhibitor ambiguity that made GO:1905594 ill-defined.
    supported_by:
      - reference_id: PMID:18254726
        supporting_text: >-
          Resveratrol was found to interact strongly with QR2 with a Kd of 39 nM
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-8936519
  qualifier: located_in
  review:
    summary: >-
      Traceable-author-statement cytosol annotation from Reactome (NQO2:FAD dimer reduces quinones
      to hydroquinones).
    action: ACCEPT
    reason: >-
      Consistent core localization; corroborates the IDA/IBA cytosol annotations.
- term:
    id: GO:0070062
    label: extracellular exosome
  evidence_type: HDA
  original_reference_id: PMID:23533145
  qualifier: located_in
  review:
    summary: >-
      High-throughput proteomic detection of NQO2 in exosomes (prostatic-secretion/urine exosome
      proteomics). Common for abundant cytosolic proteins; not evidence of a functional
      extracellular localization.
    action: KEEP_AS_NON_CORE
    reason: >-
      Mass-spectrometry detection in an exosome preparation; NQO2 is fundamentally a cytosolic
      enzyme, so this is not a functionally informative localization.
- term:
    id: GO:0070062
    label: extracellular exosome
  evidence_type: HDA
  original_reference_id: PMID:19056867
  qualifier: located_in
  review:
    summary: >-
      High-throughput proteomic detection of NQO2 in urinary exosomes.
    action: KEEP_AS_NON_CORE
    reason: >-
      Proteomics detection in exosomes; not a functional localization for this cytosolic enzyme.
core_functions:
- description: >-
    FAD-dependent cytosolic quinone reductase that uses dihydronicotinamide riboside (NRH), not
    NAD(P)H, as the electron donor to catalyze two-electron reduction of quinones to hydroquinones
    (EC 1.10.5.1; RHEA:12364). Requires FAD and a structural Zn2+; functions as a homodimer.
  molecular_function:
    id: GO:0001512
    label: dihydronicotinamide riboside quinone reductase activity
  directly_involved_in:
    - id: GO:1901662
      label: quinone catabolic process
  locations:
    - id: GO:0005829
      label: cytosol
  supported_by:
    - reference_id: PMID:10945627
      supporting_text: >-
        its activity is normally latent, and a nonbiogenic co-substrate such as NRH [nicotinamide
        riboside (reduced)] is required for enzymatic activity
suggested_questions:
- question: >-
    What are the endogenous physiological quinone substrates and the true in vivo source of the NRH
    co-substrate for NQO2, and does NQO2 predominantly detoxify quinones or, for certain substrates,
    generate more reactive/cytotoxic products?
suggested_experiments:
- description: >-
    Structure-guided separation-of-function mutants (active-site vs Zn/FAD sites) assayed for NRH:
    quinone reductase activity and for melatonin/resveratrol inhibition, to dissect the catalytic
    versus ligand-binding (MT3) roles of the active site.
- description: >-
    Metabolomic comparison of NQO2-proficient vs NQO2-null human cells challenged with model
    quinones, to determine which quinones are detoxified versus bioactivated and to test the NRH
    dependence in a cellular context.
references:
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
  reference_review:
    relevance: LOW
    correctness: MISCITED
    review_notes: >-
      The IBA propagated GO:0003955 (NAD(P)H dehydrogenase (quinone) activity, EC 1.6.5.2) to NQO2,
      but NQO2 uses NRH rather than NAD(P)H; the phylogenetic inference over-generalizes the family
      cofactor. The IBA cytosol annotation is correct.
- 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:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:10945627
  title: 'Bioactivation of 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB 1954) by human
    NAD(P)H quinone oxidoreductase 2: a novel co-substrate-mediated antitumor prodrug
    therapy.'
  findings:
  - statement: >-
      NQO2 activity is latent unless supplied with a reduced dihydronicotinamide co-substrate such
      as NRH; NAD(P)H is not the physiological electron donor.
    supporting_text: >-
      its activity is normally latent, and a nonbiogenic co-substrate such as NRH [nicotinamide
      riboside (reduced)] is required for enzymatic activity
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Establishes the NRH co-substrate requirement (the key distinction from NQO1) and the
      quinone/nitroaromatic (CB1954) reductase activity. Abstract-level cache; the NRH-dependence
      claim is anchored to the GOA IDA evidence.
- id: PMID:16189514
  title: Towards a proteome-scale map of the human protein-protein interaction network.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Large-scale interactome screen; source of a generic protein binding annotation, non-core.
- id: file:human/NQO2/NQO2-hypotheses/function-hypothesis-go-0003955/openscientist.md
  title: OpenScientist blinded function-assignment report for NQO2 (NAD(P)H dehydrogenase
    (quinone) activity, GO:0003955)
  findings:
  - statement: >-
      An independent, blinded OpenScientist run neutrally tested whether NQO2 has NAD(P)H
      dehydrogenase (quinone) activity and concluded the term is over-annotated/substrate-incorrect
      because NQO2 uses NRH rather than NAD(P)H (NAD(P)H/EC 1.6.5.2 is the NQO1 activity), pointing to
      the already-annotated GO:0001512 - concurring with this review's MODIFY.
    supporting_text: >-
      recommend REMOVAL of the IBA GO:0003955
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Blinded computational hypothesis assessment (3-iteration run) used as independent corroboration
      of the manual MODIFY (GO:0003955 -> GO:0001512), not as primary evidence. Its key claim rests on
      cached/curated primary data (NRH dependence); it additionally cites Wu et al. 1997 (PMID:9367528)
      as the definitive enzymology - a valid lead not currently in this review's reference set.
- id: PMID:15350128
  title: Crystal structure of quinone reductase 2 in complex with resveratrol.
  findings:
  - statement: >-
      Resveratrol is a potent (Kd ~35 nM) inhibitor of QR2 that binds in the active-site cleft,
      with all three of its hydroxyl groups hydrogen-bonding to QR2 residues.
    supporting_text: >-
      resveratrol is a potent inhibitor of quinone reductase 2 (QR2) activity in vitro with a
      dissociation constant of 35 nM
  - statement: >-
      The resveratrol molecule is anchored in the QR2 active site via hydrogen bonds from all
      three of its hydroxyl groups.
    supporting_text: >-
      All three resveratrol hydroxyl groups form hydrogen bonds with amino acids from QR2
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Primary structural + binding paper for the QR2-resveratrol interaction (crystal structure
      PDB 1SG0; Kd ~35 nM by tryptophan-fluorescence titration). This is the definitive
      experimental basis for resveratrol binding (GO:1905594) and is evidence-grade for a GO IDA -
      arguably the better primary reference than PMID:18254726 (which used resveratrol as an ITC
      control) - but it is not currently cited by GOA as the annotation's evidence. Added here for
      provenance/completeness, not to assert a new annotation.
- id: PMID:18254726
  title: Kinetic, thermodynamic and X-ray structural insights into the interaction
    of melatonin and analogues with quinone reductase 2.
  findings:
  - statement: >-
      QR2 is the cytosolic MT3 melatonin binding site; melatonin is a competitive active-site
      inhibitor seen in multiple orientations in the QR2 dimer.
    supporting_text: >-
      melatonin binds in multiple orientations within the active sites of the QR2 dimer as opposed
      to an allosteric site
  - statement: >-
      QR2 is a high-affinity (nanomolar) target of resveratrol, with a determined QR2:resveratrol
      crystal structure.
    supporting_text: >-
      It is one of the most potently inhibited (nanomolar) molecular targets of resveratrol, a
      natural polyphenol found in wine and peanuts, and the X-ray structure of QR2 in complex with
      resveratrol has been determined
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Primary structural/kinetic paper; source of the FAD/Zn/chloride/melatonin/resveratrol binding,
      homodimerization, and quinone-reduction IDA annotations. PMC full text verified.
- id: PMID:19056867
  title: Large-scale proteomics and phosphoproteomics of urinary exosomes.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      High-throughput exosome proteomics; source of an extracellular-exosome HDA annotation, non-core.
- id: PMID:23533145
  title: In-depth proteomic analyses of exosomes isolated from expressed prostatic
    secretions in urine.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      High-throughput exosome proteomics; source of an extracellular-exosome HDA annotation, non-core.
- id: PMID:24606901
  title: Cochaperone binding to LYR motifs confers specificity of iron sulfur cluster
    delivery.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Source of a generic protein binding annotation (HSC20/HSCB context); non-core for NQO2.
- id: PMID:25416956
  title: A proteome-scale map of the human interactome network.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Large-scale interactome screen; source of a generic protein binding annotation, non-core.
- id: PMID:31515488
  title: Extensive disruption of protein interactions by genetic variants across the
    allele frequency spectrum in human populations.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Interactome-perturbation screen; source of a generic protein binding annotation, non-core.
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      HuRI interactome map; source of a generic protein binding annotation, non-core.
- id: Reactome:R-HSA-8936519
  title: NQO2:FAD dimer reduces quinones to hydroquinones
  findings: []

NQO2

Gene Description