Nqo1 is the NADH-oxidising flavoprotein subunit (51 kDa subunit family) of the proton-pumping NADH:quinone oxidoreductase NDH-1 (respiratory complex I) of Thermus thermophilus. It sits at the tip of the peripheral arm on the cytoplasmic side of the membrane, binds NADH and the primary electron acceptor FMN, and passes electrons through its [4Fe-4S] cluster N3 into the iron-sulfur chain that ends at the quinone site. In this organism the complex reduces menaquinone and couples the reaction to proton translocation across the cytoplasmic membrane.
Definition: Catalysis of the reaction: NADH + a menaquinone + 5 H+(in) = NAD+ + a menaquinol + 4 H+(out), in which the oxidation of NADH and reduction of menaquinone are coupled to the translocation of protons across the membrane. The menaquinone counterpart of GO:0008137 NADH dehydrogenase (ubiquinone) activity, carried out by the complex I of menaquinone-using bacteria.
Justification: GO has an electrogenic NADH dehydrogenase term only for ubiquinone (GO:0008137, RHEA:29091, EC 7.1.1.2). The quinone-generic GO:0016655 does not capture the coupled proton translocation, and GO:0050136 is non-electrogenic. T. thermophilus NDH-1 reduces menaquinone and pumps protons; UniProt records its reaction against the quinone-generic, proton-coupled RHEA:57888.
Parent term: oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Nqo1 is a peripheral subunit of the membrane-bound NDH-1 on the cytoplasmic face of the cell membrane. Reason: UniProt records Nqo1 as a peripheral membrane protein of the cell membrane, cytoplasmic side, from the peripheral-arm structure (PMID:16469879). In this bacterium the cell membrane is the plasma membrane, and the subunit is held there as part of complex I. Supporting Evidence: file:THET8/nqo1/nqo1-uniprot.txt Cell membrane file:THET8/nqo1/nqo1-uniprot.txt Peripheral membrane protein |
| GO:0008137 NADH dehydrogenase (ubiquinone) activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO assigns the ubiquinone-specific complex I activity; in T. thermophilus the acceptor is menaquinone. Reason: GO:0008137 names ubiquinone as the acceptor, but UniProt states, with experimental evidence, that the immediate electron acceptor of this species' NDH-1 is menaquinone. The quinone-generic parent GO:0016655 is the honest existing term for the complex reaction, and a proton-coupled menaquinone-specific term is proposed under proposed_new_terms, and Nqo1 contributes to it as one subunit rather than catalysing it alone, which the core function records with contributes_to. The wrong enables qualifier is recorded as a source defect. Proposed replacements: oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor NADH dehydrogenase (menaquinone) activity Supporting Evidence: file:THET8/nqo1/nqo1-uniprot.txt NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. file:THET8/nqo1/nqo1-uniprot.txt The immediate electron acceptor for the enzyme in this species is menaquinone. |
| GO:0010181 FMN binding | IEA GO_REF:0000002 | ACCEPT | Summary: Nqo1 binds the non-covalent FMN that accepts the hydride from NADH. Reason: UniProt records one FMN per subunit with experimental evidence from the crystal structure of the T. thermophilus peripheral arm (PMID:16469879), whose abstract places the FMN as the primary electron acceptor. Supporting Evidence: file:THET8/nqo1/nqo1-uniprot.txt Binds 1 FMN per subunit. PMID:16469879 The primary electron acceptor, flavin-mononucleotide, is within electron transfer distance of cluster N3, leading to the main redox pathway |
| GO:0016696 oxidoreductase activity, acting on hydrogen as donor, NAD or NADP as acceptor | IEA GO_REF:0000117 | REMOVE | Summary: ARBA prediction of hydrogenase chemistry (H2 donor, NAD(P) acceptor), which Nqo1 does not perform. Reason: The term describes NAD(P)-reducing hydrogenases, which oxidise molecular hydrogen. Nqo1 is the NADH-oxidising subunit of complex I: NADH is its electron donor and quinone the final acceptor of the complex, and no hydrogenase activity is reported. The ARBA rule probably reflects the family's hydrogenase flavoprotein members (HoxF-type), so it is wrong for this protein. Supporting Evidence: file:THET8/nqo1/nqo1-uniprot.txt NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. file:THET8/nqo1/nqo1-uniprot.txt The Nqo1 subunit contains the NADH-binding site and the primary electron acceptor FMN. |
| GO:0045271 respiratory chain complex I | IEA GO_REF:0000117 | ACCEPT | Summary: Nqo1 is a core subunit of T. thermophilus NDH-1 (complex I). Reason: The prediction is ARBA-based, but the claim is independently established: UniProt records NDH-1 as composed of Nqo1 to Nqo15 with experimental evidence, and the peripheral-arm structure contains Nqo1 (PMID:16469879). The enzyme oxidises NADH and pumps protons, so it is complex I despite its menaquinone acceptor. Supporting Evidence: file:THET8/nqo1/nqo1-uniprot.txt NDH-1 is composed of 15 different subunits, Nqo1 to Nqo15. file:THET8/nqo1/nqo1-uniprot.txt NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. |
| GO:0051287 NAD binding | IEA GO_REF:0000002 | ACCEPT | Summary: Nqo1 carries the NADH-binding site of complex I. Reason: UniProt states, with experimental evidence, that Nqo1 contains the NADH-binding site, and the record maps NAD(+)-binding residues in the Rossmann-fold domain. NAD binding is part of the subunit's own chemistry. Supporting Evidence: file:THET8/nqo1/nqo1-uniprot.txt The Nqo1 subunit contains the NADH-binding site and the primary electron acceptor FMN. |
| GO:0051539 4 iron, 4 sulfur cluster binding | IEA GO_REF:0000002 | ACCEPT | Summary: Nqo1 binds cluster N3, the [4Fe-4S] cluster that takes electrons from the FMN. Reason: UniProt records one [4Fe-4S] cluster (N3) per subunit with experimental evidence from the crystal structure, and the structure places the FMN within electron transfer distance of N3 (PMID:16469879). Supporting Evidence: file:THET8/nqo1/nqo1-uniprot.txt Binds 1 [4Fe-4S] cluster per subunit. This [4Fe-4S] cluster is referred to as N3. PMID:16469879 The primary electron acceptor, flavin-mononucleotide, is within electron transfer distance of cluster N3, leading to the main redox pathway |
| GO:1902600 proton transmembrane transport | IEA GO_REF:0000108 | KEEP AS NON CORE | Summary: Inferred from the complex I activity; the complex pumps protons, but Nqo1 is a peripheral subunit with no membrane path. Reason: NDH-1 couples quinone reduction to proton translocation, so the complex takes part in proton transmembrane transport. Nqo1 sits in the soluble peripheral arm and supplies the electrons that drive the pump, not a proton path, so the process is retained as non-core context rather than as the subunit's core role. Supporting Evidence: file:THET8/nqo1/nqo1-uniprot.txt Couples the redox reaction to proton translocation |
| GO:0003954 NADH dehydrogenase activity | IC PMID:16469879 Structure of the hydrophilic domain of respiratory complex I... | NEW | Summary: Nqo1 oxidises NADH at its FMN, the subunit-level half-reaction of complex I. Reason: GO:0003954 is NADH oxidation with an unspecified acceptor, the half-reaction that takes place at this subunit's FMN within complex I. UniProt states, from the crystal structure, that Nqo1 contains the NADH-binding site and the primary electron acceptor FMN, so the inference is from structure and cofactor sites rather than from an NADH-oxidation assay on the subunit (see suggested_experiments). As in the E. coli NuoF review, the activity is recorded as contributes_to, since NADH oxidation by Nqo1 is measured only as part of the assembled enzyme. The PTHR43578 family review assesses GO:0003954 as family-wide. GOA has only the complex-level activity for this protein. Supporting Evidence: file:THET8/nqo1/nqo1-uniprot.txt The Nqo1 subunit contains the NADH-binding site and the primary electron acceptor FMN. PMID:16469879 The primary electron acceptor, flavin-mononucleotide, is within electron transfer distance of cluster N3, leading to the main redox pathway |
Loading supporting content…
Download this section (compressed HTML)Q: Should the menaquinone-reducing complex I of Thermus and other menaquinone users get a quinone-specific complex-level GO activity term, as ubiquinone users have GO:0008137?
Experiment: Measure NADH oxidation by isolated Nqo1 (or the Nqo1/Nqo2 flavoprotein subcomplex) with an artificial acceptor such as ferricyanide to confirm the subunit-level NADH dehydrogenase activity outside the assembled complex.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)