Ndk (PA3807) is the 143-aa nucleoside diphosphate kinase of Pseudomonas aeruginosa. It transfers the gamma-phosphate of ATP to other ribo- and deoxyribonucleoside diphosphates by a ping-pong mechanism through a phosphohistidine intermediate (His117), maintaining the cellular pools of GTP, UTP, CTP and dNTPs. The full-length 16-kDa enzyme is mainly cytoplasmic and non-specific; an intracellular protease generates a 12-kDa form that accumulates on the membrane in stationary phase and preferentially makes GTP, a preference also induced by complex formation with pyruvate kinase. Ndk activity is also associated with succinyl-CoA synthetase. By supplying GTP for GDP-mannose synthesis, Ndk supports production of the exopolysaccharide alginate.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004550 nucleoside diphosphate kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the 21-seed PTN000887110 IBD; ndk appears among its own sources because of its PseudoCAP IDA row, which is expected. Reason: Core activity; the node is richly seeded and the active-site His is conserved. Supporting Evidence: PMID:8809750 The cytosolic Ndk was non-specific in its transfer activity of the terminal phosphate from ATP to other nucleoside diphosphates. |
| GO:0004550 nucleoside diphosphate kinase activity | IDA PMID:8809750 Nucleoside diphosphate kinase from Pseudomonas aeruginosa: c... | ACCEPT | Summary: PseudoCAP IDA and one of 21 seeds of PTN000887110; NDK activity assayed in cell fractions. Reason: Seed verdict SOUND. Direct activity and substrate-range assays are described in the abstract. Supporting Evidence: PMID:8809750 The cytosolic Ndk was non-specific in its transfer activity of the terminal phosphate from ATP to other nucleoside diphosphates. |
| GO:0004550 nucleoside diphosphate kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: HAMAP/InterPro/EC mapping. Reason: Same claim as the IBA and IDA rows. Supporting Evidence: file:PSEAE/ndk/ndk-uniprot.txt HAMAP; MF_00451; NDP_kinase; 1. |
| GO:0005524 ATP binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: UniRule ATP-binding residues. Reason: True (ATP is the phosphate donor), but part of the kinase activity rather than a separate function. Supporting Evidence: file:PSEAE/ndk/ndk-uniprot.txt FT BINDING 11 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" |
| GO:0005737 cytoplasm | EXP PMID:8606147 Two forms of the nucleoside diphosphate kinase of Pseudomona... | ACCEPT | Summary: UniProt EXP; the 16-kDa form is predominantly cytoplasmic. Reason: Fractionation shows the full-length enzyme mainly in the cytoplasm. Supporting Evidence: PMID:8606147 The 12-kDa form was found to be predominantly associated with the P. aeruginosa cell membrane fraction, whereas the 16-kDa form was predominantly cytoplasmic. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: IBA cytoplasm from PTN000887110. Reason: Consistent with the EXP row; the cytosolic enzyme is active. Supporting Evidence: PMID:8809750 Nucleoside diphosphate kinase activity was present in both the cytosolic and membrane-associated fractions of P. aeruginosa. |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: SubCell/HAMAP mapping. Reason: Same claim as the EXP row. Supporting Evidence: PMID:8606147 The 12-kDa form was found to be predominantly associated with the P. aeruginosa cell membrane fraction, whereas the 16-kDa form was predominantly cytoplasmic. |
| GO:0006163 purine nucleotide metabolic process | IDA PMID:8809750 Nucleoside diphosphate kinase from Pseudomonas aeruginosa: c... | TOO GENERAL | Summary: PseudoCAP IDA from the NDK activity assays. Reason: True, but GO:0006183 GTP biosynthetic process, accepted here, is_a/part_of GO:0006163 and states what Ndk does. |
| GO:0006183 GTP biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: HAMAP/InterPro mapping. Reason: Ndk phosphorylates GDP to GTP; the membrane form prefers GTP synthesis. Supporting Evidence: PMID:8606147 In the membrane-associated state, the 12-kDa form of Ndk was found to synthesize GTP in preference to other nucleoside triphosphates. |
| GO:0006220 pyrimidine nucleotide metabolic process | IDA PMID:8809750 Nucleoside diphosphate kinase from Pseudomonas aeruginosa: c... | TOO GENERAL | Summary: PseudoCAP IDA from the NDK activity assays. Reason: True, but GO:0006228 UTP and GO:0006241 CTP biosynthetic process, accepted here, fall under GO:0006220 and state what Ndk does. |
| GO:0006228 UTP biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: HAMAP/InterPro mapping. Reason: The cytosolic enzyme phosphorylates NDPs non-specifically, including UDP. Supporting Evidence: PMID:8809750 The cytosolic Ndk was non-specific in its transfer activity of the terminal phosphate from ATP to other nucleoside diphosphates. |
| GO:0006241 CTP biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: HAMAP/InterPro mapping. Reason: The cytosolic enzyme phosphorylates NDPs non-specifically, including CDP. Supporting Evidence: PMID:8809750 The cytosolic Ndk was non-specific in its transfer activity of the terminal phosphate from ATP to other nucleoside diphosphates. |
| GO:0009142 nucleoside triphosphate biosynthetic process | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from PTN000887110; sound at the node. Reason: True, but the GTP, UTP and CTP biosynthetic terms accepted here are is_a descendants of GO:0009142, so the inherited term adds nothing for this gene. |
| GO:0042121 alginic acid biosynthetic process | IDA PMID:8809750 Nucleoside diphosphate kinase from Pseudomonas aeruginosa: c... | REMOVE | Summary: PseudoCAP IDA. The abstract reports that ndk hyperexpression partially restored alginate production in an algR2 regulatory mutant. Reason: Ndk performs no step of alginate synthesis; it supplies GTP, a co-substrate that the GDP-mannose pyrophosphorylase AlgA consumes. The evidence is a partial rescue of a pleiotropic regulatory mutant, a precursor-supply phenotype, and the authors' own link is through GTP availability. Necessity of a co-substrate is not participation. This row is not a PAINT seed. Supporting Evidence: PMID:8809750 Hyperexpression of ndk from pGWS95 in the P. aeruginosa algR2 mutant also restored alginate production to levels that were approximately 60% of wild type. PMID:8809750 The significance of GTP in signal transduction events within the cell and in the production of GDP-mannose, an essential alginate precursor, clearly indicates the importance of Ndk in cellular processes as well as in alginate synthesis. |
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Download this section (compressed HTML)Q: Is the 12-kDa membrane-associated, GTP-preferring form of Ndk physiologically important, and which protease generates it (elastase has been proposed)?
Experiment: Measure GTP pools and alginate in a clean ndk deletion of a mucoid strain, with and without a GTP-preferring truncated ndk allele, to separate precursor supply from regulatory effects.
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