Bacterial respiratory complex I (proton-translocating NADH:quinone oxidoreductase)

Reusable bacterial module for the conserved 14-subunit respiratory complex I, also called NDH-1 or NADH:quinone oxidoreductase. The peripheral arm oxidizes NADH, transfers electrons through FMN and iron-sulfur centers, and reduces the quinone pool. The membrane arm couples this redox chemistry to proton translocation. The module separates the NADH-input, quinone-reduction, membrane-interface, and antiporter-like proton-pumping parts so that fused subunits such as NuoC/D can be represented without collapsing the enzyme to a single step. It excludes the non-homologous, non-proton-pumping type-II NADH dehydrogenase (Ndh/NDH-2).

The 14-subunit NDH-1 core is conserved across proteobacteria and other bacterial phyla, so the module is written at the family level and grounded with two experimentally anchored gammaproteobacterial exemplar sets: the Escherichia coli K-12 NuoA-N complex, the best-characterized bacterial complex I genetically and biochemically, and the single-copy Pseudomonas putida KT2440 PP_4119-PP_4131 nuo locus. In both exemplars NuoC and NuoD are fused into one polypeptide (E. coli P33599, P. putida Q88FH5), so 13 proteins supply the 14 conserved subunit roles; in lineages with separate C and D subunits (for example Thermus thermophilus Nqo5 and Nqo4) the fused annoton is satisfied by the two polypeptides together. The fused-annoton grounding, PANTHER:PTHR11993, is the NuoD/49-kDa family; a separate NuoC/30-kDa polypeptide belongs to a different family that is not grounded here. Thermus Nqo subunits, which provided the first complete complex I structures, were not added as a third exemplar set because they would add 14 more members without adding a module role. PANTHER groundings were adopted from the module-wide grounding pass and checked against the PANTHER 19.0 member index: each exemplar falls in the cited family, except that PANTHER's own classification file places E. coli NuoF in PTHR11780:SF10 (with mitochondrial NDUFV1) while UniProt and InterPro place E. coli and P. putida NuoF in PTHR43578:SF3. The tree placement is adopted for E. coli NuoF (recorded in interpro/panther/panther-members-overrides.tsv), while P. putida NuoF, which PANTHER's files do not classify, stays in PTHR43578 by its UniProt cross-reference; the NuoF annoton is therefore grounded to both families, and the PTHR43578 and PTHR11780 reviews describe the split. NuoG is grounded at subfamily PTHR43105:SF10 rather than the family, because PTHR43105 is dominated by molybdopterin oxidoreductase catalytic subunits (nitrate reductases, formate dehydrogenases) for which a family-wide electron-transfer-subunit claim does not hold. Mitochondrial complex I, with its eukaryotic supernumerary NDUF subunits, is modelled separately (mitochondrial_complex_i_core); absence of those subunits here is not a pathway hole. GO:0050136 denotes non-electrogenic NADH:quinone activity and is incompatible with the defining proton-translocating chemistry of NDH-1; its automated propagation to Nuo subunits is removed in the exemplar gene reviews rather than used to model this module. The two terms are siblings, not parent and child: in GO, GO:0008137 NADH dehydrogenase (ubiquinone) activity (RHEA:29091, EC 7.1.1.2, with 4 H+ translocated per NADH) and GO:0050136 (RHEA:46160, EC 1.6.5.9) are each is_a GO:0003954 NADH dehydrogenase activity, and GO:0008137 is not an is_a descendant of GO:0050136 (checked against the GO release in the local OAK database, 2026-11-02).