Ppk (polyphosphate kinase 1, VPARA_28600) in Variovorax paradoxus is a 710-amino-acid cytosolic kinase (EC 2.7.4.1; HAMAP rule MF_00347, InterPro IPR003414) that catalyzes the reversible transfer of the terminal gamma-phosphate of ATP to synthesize long-chain inorganic polyphosphate (polyP) via a phosphohistidine intermediate at His441, using Mg(2+) bound at Glu381 as an essential cofactor.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006799 polyphosphate biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Reason: VPARA_28600 (A0A0H2M4T4) is a canonical 710-residue PPK1 enzyme (HAMAP MF_00347, InterPro IPR003414) that synthesizes long-chain inorganic polyphosphate from ATP. Supporting Evidence: UniProtKB:A0A0H2M4T4 CC -!- FUNCTION: Catalyzes the reversible transfer of the terminal phosphate CC of ATP to form a long-chain polyphosphate (polyP). {ECO:0000256|HAMAP- CC Rule:MF_00347, ECO:0000256|RuleBase:RU003800}. |
| GO:0008976 polyphosphate kinase activity | IEA GO_REF:0000120 | ACCEPT | Reason: VPARA_28600 carries the complete PPK1 domain architecture and conserved catalytic phosphohistidine residue His441 required for polyphosphate kinase activity (EC 2.7.4.1, RHEA:19573). Supporting Evidence: UniProtKB:A0A0H2M4T4 FT ACT_SITE 441 FT /note="Phosphohistidine intermediate" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00347" |
| GO:0009358 polyphosphate kinase complex | IEA GO_REF:0000002 | ACCEPT | Reason: Bacterial PPK1 enzymes (InterPro IPR003414) assemble into a functional oligomeric polyphosphate kinase complex. Supporting Evidence: UniProtKB:A0A0H2M4T4 DR InterPro; IPR003414; PP_kinase. |
| GO:0005524 ATP binding | IC UniProtKB:A0A0H2M4T4 | NEW | Reason: Inferred by curator (IC) from polyphosphate kinase activity (GO:0008976) and the conserved ATP-binding site (Asn55, Arg378, Lys429, Arg571) annotated by HAMAP rule MF_00347. Supporting Evidence: UniProtKB:A0A0H2M4T4 FT BINDING 55 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00347" |
| GO:0000287 magnesium ion binding | IC UniProtKB:A0A0H2M4T4 | NEW | Reason: Inferred by curator (IC) because VPARA_28600 coordinates Mg(2+) at conserved residue Glu381 (HAMAP rule MF_00347) as an essential cofactor for phosphoryl transfer. Supporting Evidence: UniProtKB:A0A0H2M4T4 FT BINDING 381 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00347" |
| GO:0005829 cytosol | IC UniProtKB:A0A0H2M4T4 | NEW | Reason: Inferred by curator (IC) because VPARA_28600 is a soluble intracellular enzyme lacking signal peptides or transmembrane helices that synthesizes inorganic polyphosphate in the bacterial cytosol. Supporting Evidence: UniProtKB:A0A0H2M4T4 CC -!- FUNCTION: Catalyzes the reversible transfer of the terminal phosphate CC of ATP to form a long-chain polyphosphate (polyP). {ECO:0000256|HAMAP- CC Rule:MF_00347, ECO:0000256|RuleBase:RU003800}. |
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Download this section (compressed HTML)Q: Does overexpression of ppk (VPARA_28600) or deletion of exopolyphosphatase (ppx) increase intracellular heavy-metal or lanthanide bioaccumulation capacity in Variovorax paradoxus?
Experiment: Compare intracellular polyP granule formation (DAPI fluorescence shift and TEM-EDS) and metal/lanthanide cation sequestration between wild-type Variovorax paradoxus and a delta-ppk mutant.
Hypothesis: Loss of ppk eliminates intracellular polyP granules and reduces intracellular polyphosphate-mediated metal cation sequestration.
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