Gcd (quinoprotein glucose dehydrogenase, VPARA_65850) in Variovorax paradoxus is an 818-amino-acid inner-membrane PQQ-dependent glucose dehydrogenase (EC 1.1.5.2; NCBIfam TIGR03074, InterPro IPR017511) comprising five N-terminal transmembrane alpha-helices (residues 14-147) that bind ubiquinone and a C-terminal periplasmic beta-propeller catalytic domain that binds pyrroloquinoline quinone (PQQ) and divalent cations. It catalyzes the direct periplasmic oxidation of D-glucose to D-glucono-1,5-lactone (which hydrolyzes to D-gluconate/gluconic acid) coupled to ubiquinone reduction in the respiratory chain.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0008876 quinoprotein glucose dehydrogenase activity | IEA GO_REF:0000120 | ACCEPT | Reason: VPARA_65850 (A0A0H2LUW4) is a full-length 818-residue membrane-bound PQQ-dependent quinoprotein glucose dehydrogenase (EC 1.1.5.2; NCBIfam TIGR03074 PQQ_membr_DH, InterPro IPR017511, PANTHER PTHR32303:SF4) that oxidizes D-glucose to D-glucono-1,5-lactone using ubiquinone as electron acceptor. Supporting Evidence: UniProtKB:A0A0H2LUW4 DR NCBIfam; TIGR03074; PQQ_membr_DH; 1. UniProtKB:A0A0H2LUW4 DR PANTHER; PTHR32303:SF4; QUINOPROTEIN GLUCOSE DEHYDROGENASE; 1. |
| GO:0016020 membrane | IEA GO_REF:0000002 | MODIFY | Reason: The broad term membrane (GO:0016020) should be refined to plasma membrane (GO:0005886), as bacterial PQQ-dependent membrane glucose dehydrogenase (TIGR03074) is anchored in the inner (plasma) membrane via five N-terminal transmembrane alpha-helices with its catalytic domain facing the periplasm. Proposed replacements: plasma membrane Supporting Evidence: UniProtKB:A0A0H2LUW4 FT TRANSMEM 14..38 FT /note="Helical" FT /evidence="ECO:0000256|SAM:Phobius" |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000117 | TOO GENERAL | Reason: Generic oxidoreductase activity (GO:0016491) is true of Gcd but uninformative because the specific term quinoprotein glucose dehydrogenase activity (GO:0008876) is already accepted on this record. Supporting Evidence: UniProtKB:A0A0H2LUW4 DR PANTHER; PTHR32303:SF4; QUINOPROTEIN GLUCOSE DEHYDROGENASE; 1. |
| GO:0016614 oxidoreductase activity, acting on CH-OH group of donors | IEA GO_REF:0000002 | TOO GENERAL | Reason: The parent term oxidoreductase activity, acting on CH-OH group of donors (GO:0016614) is true of Gcd but subsumed by the specific child term quinoprotein glucose dehydrogenase activity (GO:0008876) already accepted on this record. Supporting Evidence: UniProtKB:A0A0H2LUW4 DR NCBIfam; TIGR03074; PQQ_membr_DH; 1. |
| GO:0048038 quinone binding | IEA GO_REF:0000002 | ACCEPT | Reason: Membrane-bound PQQ-dependent glucose dehydrogenase (TIGR03074 / IPR017511) binds membrane ubiquinone via its N-terminal five-helix transmembrane domain to transfer electrons directly to the respiratory chain. Supporting Evidence: UniProtKB:A0A0H2LUW4 DR InterPro; IPR017511; PQQ_mDH. |
| GO:0019521 D-gluconate metabolic process | IC UniProtKB:A0A0H2LUW4 | NEW | Reason: Inferred by curator (IC) from its quinoprotein glucose dehydrogenase activity (GO:0008876, TIGR03074): periplasmic oxidation of D-glucose to D-glucono-1,5-lactone (which hydrolyzes to D-gluconate) is the direct step initiating D-gluconate metabolism. Supporting Evidence: UniProtKB:A0A0H2LUW4 DR NCBIfam; TIGR03074; PQQ_membr_DH; 1. |
Loading supporting content…
Download this section (compressed HTML)Q: Does Variovorax paradoxus synthesize pyrroloquinoline quinone (PQQ) de novo under low-phosphate or mineral-leaching conditions, or can it scavenge exogenous PQQ from co-occurring rhizosphere bacteria?
Experiment: Generate a clean deletion of gcd (VPARA_65850) in Variovorax paradoxus and quantify extracellular gluconic acid production, pH drop, and mineral phosphate or lanthanide solubilization from refractory ores by ICP-MS.
Hypothesis: Deletion of gcd abolishes periplasmic gluconic acid production and reduces organic-acid-mediated mineral solubilization.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)