ndk1 (SPAC806.07) is the nucleoside diphosphate kinase of fission yeast, a 151-residue homotrimeric NDK-family enzyme about 60% identical to budding-yeast Ynk1 and mammalian NME proteins. Using a phosphohistidine (His117) ping-pong mechanism it transfers the gamma-phosphate of ATP to ribo- and deoxyribonucleoside diphosphates, producing UTP, CTP, GTP and dNTPs; in pyrimidine synthesis it converts UDP (from ura6) to UTP. Disruption of ndk1 strongly reduces cellular NDK activity but is not lethal and has no obvious growth or mating phenotype, whereas a catalytically dead C116 allele acts as a dominant negative inhibitor of sexual development and pheromone-induced gene expression. The protein is mainly cytosolic, with nuclear signal in a genome-wide screen and a possible minor mitochondrial pool inferred from Ynk1.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004550 nucleoside diphosphate kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PANTHER PTN000887110 (NDK clade; donors include S. cerevisiae YNK1, human NME1/NME2, and S. pombe ndk1 itself, reflecting its own experimental annotation). ndk1 is the sole canonical NDK in S. pombe and retains the active-site His117. Reason: Core activity; phylogenetic inference grounded in ndk1's own experimental data. Supporting Evidence: file:SCHPO/ndk1/ndk1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- PMID:7499258 The gene product exhibited NDK activity and cross-reacted with antibodies raised against rat NDK. |
| GO:0004550 nucleoside diphosphate kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (InterPro IPR001564 + EC:2.7.4.6). Correct; redundant with the IMP and IBA rows. Reason: Correct electronic MF. Supporting Evidence: file:SCHPO/ndk1/ndk1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- file:SCHPO/ndk1/ndk1-uniprot.txt Reaction=a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'- |
| GO:0004550 nucleoside diphosphate kinase activity | IMP PMID:7499258 Cloning and functional analysis of the ndk1 gene encoding nu... | ACCEPT | Summary: IMP from Izumiya and Yamamoto 1995 (PMID:7499258): the cloned ndk1 product had NDK activity, ndk1 disruption greatly reduced cellular NDK activity, and a C116 point mutant next to the catalytic His117 was inactive. Direct S. pombe evidence for the activity. Reason: Experimental S. pombe evidence for the core activity. Supporting Evidence: PMID:7499258 The gene product exhibited NDK activity and cross-reacted with antibodies raised against rat NDK. PMID:7499258 Disruption of ndk1 greatly reduced the cellular NDK activity but caused no obvious phenotype in cell growth and sexual development of the organism. PMID:7499258 the mutant gene product showed no NDK activity |
| GO:0005634 nucleus | HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ... | KEEP AS NON CORE | Summary: PomBase HDA from the ORFeome GFP screen (PMID:16823372). NDKs are small soluble proteins that commonly appear in both cytoplasm and nucleus in GFP screens; no specific nuclear function has been shown for S. pombe ndk1. Reason: High-throughput localization; plausible minor pool, not part of the core metabolic role. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000887110 for cytoplasm. Consistent with the S. pombe cytosol HDA and with cytosolic YNK1. Reason: Correct; cytosol is the more precise term. |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA from PTN000142925 (donors include S. cerevisiae YNK1 and human NME4, the mitochondrial isoform). In budding yeast a small fraction of Ynk1 resides in the mitochondrial intermembrane space; no S. pombe mitochondrial localization data exist and ndk1 has no predicted targeting signal noted by UniProt. Reason: Plausible minor mitochondrial pool by inheritance from YNK1; unverified in S. pombe, so non-core. Supporting Evidence: PMID:12472466 we demonstrate that in Saccharomyces cerevisiae a small fraction of total NDPK activity encoded by YNK1 is present in the intermembrane space (IMS) of mitochondria |
| GO:0005758 mitochondrial intermembrane space | ISO GO_REF:0000024 | KEEP AS NON CORE | Summary: ISO from S. cerevisiae YNK1 (SGD:S000001550), which has a small IMS-localized fraction. Transfer to S. pombe is reasonable given ~60% identity, but untested. Reason: Ortholog-based minor location; non-core pending S. pombe evidence. Supporting Evidence: PMID:12472466 we demonstrate that in Saccharomyces cerevisiae a small fraction of total NDPK activity encoded by YNK1 is present in the intermembrane space (IMS) of mitochondria |
| GO:0005829 cytosol | HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ... | ACCEPT | Summary: PomBase HDA (cytosol) from the ORFeome GFP screen. Cytosol is where NDK phosphorylates UDP/CDP/GDP and dNDPs; it is the location used for ndk1 activities in PomBase GO-CAMs 69a0c46f00003691 and 6796b94c00000009. Reason: Main compartment of the enzyme. |
| GO:0006183 GTP biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO (IPR001564) to GTP biosynthetic process. NDK converts GDP to GTP using ATP; broad specificity makes this a legitimate product-level process, as accepted for YNK1. Reason: Correct consequence of broad NDP kinase specificity. Supporting Evidence: file:SCHPO/ndk1/ndk1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0006228 UTP biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO (IPR001564) to UTP biosynthetic process. UDP to UTP is the ndk1 step in pyrimidine nucleotide synthesis, and PomBase GO-CAM 69a0c46f00003691 places ndk1 NDK activity part_of UTP biosynthesis. Reason: Precise process for the pyrimidine-pathway role. Supporting Evidence: file:SCHPO/ndk1/ndk1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP |
| GO:0006241 CTP biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO (IPR001564) to CTP biosynthetic process. NDK phosphorylates CDP to CTP (salvage route); CTP from UTP is made by CTP synthase. Correct for the CDP to CTP reaction. Reason: Correct consequence of NDP kinase activity on CDP. Supporting Evidence: file:SCHPO/ndk1/ndk1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0006241 CTP biosynthetic process | IMP PMID:7499258 Cloning and functional analysis of the ndk1 gene encoding nu... | ACCEPT | Summary: IMP from PMID:7499258 (PomBase). The abstract shows reduced cellular NDK activity on ndk1 disruption; the full text (not cached) presumably supports the CTP-specific call. PomBase also uses CTP biosynthetic process for ndk1 in GO-CAMs 69a0c46f00003691 and 6796b94c00000009. Deferring to the curator. Reason: Experimental annotation from full text not available here; consistent with enzyme activity. Supporting Evidence: PMID:7499258 Disruption of ndk1 greatly reduced the cellular NDK activity but caused no obvious phenotype in cell growth and sexual development of the organism. |
| GO:0009142 nucleoside triphosphate biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000887110 (includes ndk1 itself as a donor) for nucleoside triphosphate biosynthetic process; the best general description of a broad-specificity NDP kinase, matching the UniProt function statement. Reason: Accurate general process; core. Supporting Evidence: file:SCHPO/ndk1/ndk1-uniprot.txt FUNCTION: Major role in the synthesis of nucleoside triphosphates other |
| GO:0009142 nucleoside triphosphate biosynthetic process | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA rule (ARBA00033837) IEA to nucleoside triphosphate biosynthetic process; redundant with IBA. Reason: Correct electronic process. Supporting Evidence: file:SCHPO/ndk1/ndk1-uniprot.txt FUNCTION: Major role in the synthesis of nucleoside triphosphates other |
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Download this section (compressed HTML)Q: Since ndk1 deletion is viable with greatly reduced NDK activity, which enzyme(s) supply residual UTP/CTP/dNTP formation in S. pombe (e.g. adenylate kinases or other NDP-phosphorylating activities)?
Q: Does a fraction of S. pombe ndk1 localize to the mitochondrial intermembrane space as Ynk1 does in budding yeast?
Experiment: Measure NTP/dNTP pools and residual NDP kinase activity in ndk1 deletion cells, and test synthetic lethality with adenylate kinase genes.
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