FdnG (PA4812) is the large catalytic (alpha) subunit of the membrane-bound, nitrate-inducible respiratory formate dehydrogenase of Pseudomonas aeruginosa, encoded in the fdnGHI cluster with the iron-sulfur subunit FdnH (PA4811) and the cytochrome b subunit FdnI (PA4810). It belongs to the prokaryotic molybdopterin-containing oxidoreductase family, carries an N-terminal [4Fe-4S]-binding domain and a molybdenum bis(molybdopterin guanine dinucleotide) cofactor domain, and has a twin-arginine (Tat) signal peptide, so it is exported to the periplasmic face of the cytoplasmic membrane. There it oxidises formate to CO2 and passes the electrons through FdnH and FdnI to the quinone pool. The enzyme is made during anaerobic growth on nitrate, when it and nitrate reductase form a short formate-to-nitrate respiratory chain.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0008863 formate dehydrogenase (NAD+) activity | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO NAD+-dependent formate dehydrogenase activity from the FdnG alpha-subunit signature. Reason: FdnG is the Mo-bisMGD catalytic subunit of a membrane-bound, Tat-exported respiratory formate dehydrogenase that donates electrons to the quinone pool via FdnH and FdnI, not to NAD+. The purified P. aeruginosa enzyme sits in a membrane particle with nitrate reductase as a short respiratory chain. The NAD+ term describes a different, cytoplasmic class of formate dehydrogenase, so the IPR006443 mapping to it is wrong for this family. Supporting Evidence: PMID:3038081 The separation of the FDH enzyme from nitrate reductase (NiR), which are found together in a particle fraction and constitute the short respiratory chain of this bacterium file:PSEAE/fdnG/fdnG-uniprot.txt NCBIfam; TIGR01553; formate-DH-alph |
| GO:0009055 electron transfer activity | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA electron transfer activity from PTN000745948, seeded by E. coli FdnG (P24183). Reason: The FdnG [4Fe-4S] cluster relays electrons from the Mo-bisMGD site towards FdnH, so the subunit does transfer electrons, but its defining activity is formate oxidation. E. coli FdnG carries this term by IDA, and the node term suits the FdnG clade. Supporting Evidence: file:PSEAE/fdnG/fdnG-uniprot.txt PROSITE; PS51669; 4FE4S_MOW_BIS_MGD; 1. |
| GO:0009055 electron transfer activity | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO electron transfer activity from the FdnG signature. Reason: Same claim as the IBA row; true for the [4Fe-4S]-containing catalytic subunit but secondary to its formate dehydrogenase activity. Supporting Evidence: file:PSEAE/fdnG/fdnG-uniprot.txt PROSITE; PS51669; 4FE4S_MOW_BIS_MGD; 1. |
| GO:0009061 anaerobic respiration | IBA GO_REF:0000033 | ACCEPT | Summary: IBA anaerobic respiration from E. coli FdnG and FdoG. Reason: The P. aeruginosa enzyme was purified after anaerobic growth on nitrate and forms the formate-to-nitrate respiratory chain with nitrate reductase; FdnG catalyses the electron donor step of that chain. Supporting Evidence: PMID:3038081 The purification of formate dehydrogenase (FDH) from Pseudomonas aeruginosa after anaerobic growth on nitrate-containing medium was carried out. |
| GO:0009061 anaerobic respiration | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA anaerobic respiration. Reason: Same claim as the IBA row; supported by the P. aeruginosa purification paper. Supporting Evidence: PMID:3038081 The purification of formate dehydrogenase (FDH) from Pseudomonas aeruginosa after anaerobic growth on nitrate-containing medium was carried out. |
| GO:0009326 formate dehydrogenase complex | IBA GO_REF:0000033 | ACCEPT | Summary: IBA formate dehydrogenase complex from the E. coli FdnG/FdoG seeds. Reason: FdnG is the catalytic subunit of the FdnGHI complex; the purified P. aeruginosa FDH contained Mo, [4Fe-4S] and a bis-histidine haem, the cofactor set of an alpha-beta-gamma FDH-N complex. Supporting Evidence: PMID:3038081 These techniques have allowed the haem, iron-sulphur clusters and molybdenum components to be detected |
| GO:0009326 formate dehydrogenase complex | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA formate dehydrogenase complex. Reason: Same claim as the IBA row. Supporting Evidence: PMID:3038081 These techniques have allowed the haem, iron-sulphur clusters and molybdenum components to be detected |
| GO:0015944 formate oxidation | IBA GO_REF:0000033 | ACCEPT | Summary: IBA formate oxidation. Reason: FdnG carries the formate-oxidising Mo-bisMGD active site; the purified P. aeruginosa FDH oxidised formate in a dye-reduction assay. Supporting Evidence: PMID:3038081 Addition of sodium dithionite maintained the activity of the enzyme, even after subsequent exposure to air, in an assay involving formate reduction with Nitro Blue Tetrazolium as reductant. |
| GO:0015944 formate oxidation | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA formate oxidation. Reason: Same claim as the IBA row. Supporting Evidence: PMID:3038081 Addition of sodium dithionite maintained the activity of the enzyme, even after subsequent exposure to air, in an assay involving formate reduction with Nitro Blue Tetrazolium as reductant. |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: Generic oxidoreductase activity from molybdopterin oxidoreductase domain signatures. Reason: True but uninformative; GO:0036397 formate dehydrogenase (quinone) activity, accepted below, is an is_a descendant of GO:0016491. |
| GO:0036397 formate dehydrogenase (quinone) activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000745948 (FdnG/FdoG clade, 3 seeds, 16 leaf IBAs). Seeds are E. coli FdnG (P24183, IDA PMID:1099093) and FdoG (P32176, IDA PMID:1504073) plus this gene (PseudoCAP IDA, PMID:3038081). Reason: The node term suits a clade of membrane-bound, quinone-reducing FDH catalytic subunits, and the IBD stands on the two E. coli seeds alone. FdnG's own IDA row (SOUND seed) is expected among the WITH/FROM entities. Supporting Evidence: PMID:3038081 The separation of the FDH enzyme from nitrate reductase (NiR), which are found together in a particle fraction and constitute the short respiratory chain of this bacterium |
| GO:0036397 formate dehydrogenase (quinone) activity | IDA PMID:3038081 Purification and properties of formate dehydrogenase from Ps... | ACCEPT | Summary: PseudoCAP IDA, the PTN000745948 seed row. Formate dehydrogenase was purified from nitrate-grown anaerobic P. aeruginosa membranes and assayed with a tetrazolium dye; the preparation contained Mo, [4Fe-4S] and a bis-histidine cytochrome b. Reason: Seed verdict SOUND. The activity measured is that of the purified FDH complex, of which FdnG is the catalytic subunit. The assay used an artificial acceptor, but the abstract places the enzyme in a membrane respiratory chain with nitrate reductase, which takes electrons from quinol, so the quinone-linked term is the right reading. The 1987 paper does not name genes; attribution to PA4812 rests on fdnGHI being the only FDH-N-type cluster in PAO1 and the matching cofactor set (I could read only the abstract). This is a biochemical assay of a purified complex, not an operon-level mutant phenotype. Supporting Evidence: PMID:3038081 The separation of the FDH enzyme from nitrate reductase (NiR), which are found together in a particle fraction and constitute the short respiratory chain of this bacterium PMID:3038081 In its purest state FDH contains one molecule of cytochrome co-ordinated by two histidine ligands in the oxidized state. |
| GO:0036397 formate dehydrogenase (quinone) activity | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA formate dehydrogenase (quinone) activity. Reason: Same claim as the IDA and IBA rows. Supporting Evidence: PMID:3038081 The separation of the FDH enzyme from nitrate reductase (NiR), which are found together in a particle fraction and constitute the short respiratory chain of this bacterium |
| GO:0042597 periplasmic space | IEA GO_REF:0000044 | ACCEPT | Summary: Periplasm from the UniProt subcellular-location mapping. Reason: FdnG has a twin-arginine signal peptide and, as in E. coli FDH-N, faces the periplasm while held on the membrane by FdnI; formate is oxidised on the periplasmic side. Supporting Evidence: file:PSEAE/fdnG/fdnG-uniprot.txt PROSITE; PS51318; TAT; 1. file:PSEAE/fdnG/fdnG-uniprot.txt SIGNAL 1..33 |
| GO:0043546 molybdopterin cofactor binding | IEA GO_REF:0000002 | ACCEPT | Summary: Molybdopterin cofactor binding from molybdopterin dinucleotide-binding domain signatures. Reason: FdnG has the molybdopterin and molybdopterin-dinucleotide-binding domains, and molybdenum was detected in the purified P. aeruginosa FDH. Supporting Evidence: file:PSEAE/fdnG/fdnG-uniprot.txt Pfam; PF01568; Molydop_binding; 1. PMID:3038081 These techniques have allowed the haem, iron-sulphur clusters and molybdenum components to be detected |
| GO:0045333 cellular respiration | IEA GO_REF:0000002 | TOO GENERAL | Summary: Cellular respiration from the FdnG signature. Reason: True but uninformative; GO:0009061 anaerobic respiration, accepted in this review, is an is_a descendant of GO:0045333. |
| GO:0047111 formate dehydrogenase (cytochrome-c-553) activity | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO formate dehydrogenase (cytochrome-c-553) activity. Reason: The FdnGHI enzyme passes electrons from formate through FdnH to the cytochrome b of FdnI and on to quinone; there is no cytochrome c subunit or cytochrome c acceptor in this complex. The purified P. aeruginosa FDH lost contaminating cytochrome c as it was purified, and its purest form contains only a bis-histidine cytochrome. The mapping of IPR006443 to the cytochrome c-553 enzyme (a different, Desulfovibrio-type FDH) is wrong for this family. Supporting Evidence: PMID:3038081 The preparations vary in the amount of contaminating nitrate reductase, the amount of cytochrome c present and the concentration of oxidized [3Fe-4S] cluster. PMID:3038081 In its purest state FDH contains one molecule of cytochrome co-ordinated by two histidine ligands in the oxidized state. |
| GO:0051539 4 iron, 4 sulfur cluster binding | IEA GO_REF:0000120 | ACCEPT | Summary: 4Fe-4S cluster binding from the molybdopterin oxidoreductase 4Fe-4S domain. Reason: FdnG has the N-terminal 4Fe-4S Mo/W bis-MGD domain with four cysteine ligands, and a [4Fe-4S]+ cluster was detected in the purified P. aeruginosa FDH. Supporting Evidence: file:PSEAE/fdnG/fdnG-uniprot.txt PROSITE; PS51669; 4FE4S_MOW_BIS_MGD; 1. PMID:3038081 The e.p.r. and m.c.d. spectra of the reduced state of FDH reveal the presence of an iron-sulphur cluster of the [4Fe-4S]+ type. |
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Experiment: Assay formate:quinone oxidoreductase activity (with a ubiquinone analogue) in membranes of a PAO1 fdnG deletion mutant and its complemented strain grown anaerobically on nitrate.
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