YNK1 encodes the single nucleoside diphosphate kinase (NDPK, EC 2.7.4.6) of Saccharomyces cerevisiae, the yeast homologue of human NME1/NM23. The homo-oligomeric enzyme transfers the gamma-phosphate of a nucleoside triphosphate (normally ATP) to any ribo- or deoxyribonucleoside diphosphate via a ping-pong mechanism with a phosphohistidine intermediate, producing the UTP, CTP, GTP and dNTPs needed for RNA and DNA synthesis; it has broad specificity, with dTDP, CDP and UDP among the best acceptors in vitro. Ynk1 is predominantly cytosolic, with a small fraction imported into the mitochondrial intermembrane space, where it has been proposed to supply GTP to IMS proteins. YNK1 is not essential, consistent with redundant NDP-phosphorylating activities in yeast, but ynk1 mutants show delayed repair of UV- and etoposide-induced nuclear DNA damage and an elevated mutation rate.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004550 nucleoside diphosphate kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT node PTN000887110 (NDK family incl. human NME1/2, E. coli Ndk); correct, Ynk1's own experimental annotations are among the descendants. Supporting Evidence: PMID:1659321 Nucleoside-diphosphate kinase is an enzyme which catalyzes the phosphorylation of nucleoside diphosphates into the corresponding triphosphates for nucleic acid biosynthesis file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0004550 nucleoside diphosphate kinase activity | IDA PMID:12472466 Nucleoside diphosphate kinase of Saccharomyces cerevisiae, Y... | ACCEPT | Summary: Amutha & Pain measured NDPK activity encoded by YNK1 in cytosolic and mitochondrial IMS fractions; direct 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 PMID:12472466 It catalyses the transfer of gamma phosphates from nucleoside triphosphates to nucleoside diphosphates by a mechanism that involves formation of an autophosphorylated enzyme intermediate |
| GO:0004550 nucleoside diphosphate kinase activity | IDA PMID:5793714 Kinetic studies of yeast nucleoside diphosphate kinase. | ACCEPT | Summary: Garces & Cleland 1969 kinetic study of yeast NDPK (ping-pong mechanism per UniProt); abstract not available in cache, but the activity is unambiguous. Defer to curator. Supporting Evidence: PMID:5793714 Kinetic studies of yeast nucleoside diphosphate kinase file:yeast/YNK1/YNK1-uniprot.txt FUNCTION: Major role in the synthesis of nucleoside triphosphates other |
| GO:0004550 nucleoside diphosphate kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: InterPro NDK (IPR001564) / EC 2.7.4.6 mapping; correct. Supporting Evidence: file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0004550 nucleoside diphosphate kinase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways superpathway of purine nucleotides de novo biosynthesis II: Ynk1 catalyses GDP, dADP and dGDP phosphorylation. NDPK activity is correct regardless of which pathway context generated the row. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0004550 nucleoside diphosphate kinase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways de novo biosynthesis of purine nucleotides: Ynk1 catalyses GDP, dADP and dGDP phosphorylation. NDPK activity is correct regardless of which pathway context generated the row. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0004550 nucleoside diphosphate kinase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways superpathway of histidine, purine, and pyrimidine biosynthesis: Ynk1 catalyses GDP, dADP and dGDP phosphorylation (and UDP/CDP via the pyrimidine sub-pathways). NDPK activity is correct regardless of which pathway context generated the row. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0004550 nucleoside diphosphate kinase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways superpathway of guanosine nucleotides de novo biosynthesis II: Ynk1 catalyses GDP and dGDP phosphorylation. NDPK activity is correct regardless of which pathway context generated the row. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0004550 nucleoside diphosphate kinase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways superpathway of adenosine nucleotides de novo biosynthesis II: Ynk1 catalyses dADP + ATP -> dATP. NDPK activity is correct regardless of which pathway context generated the row. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0004550 nucleoside diphosphate kinase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways UTP and CTP de novo biosynthesis: Ynk1 catalyses UDP + ATP -> UTP (UDPKIN-RXN, which has no gene in YeastCyc itself). NDPK activity is correct regardless of which pathway context generated the row. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0004550 nucleoside diphosphate kinase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways adenosine deoxyribonucleotides de novo biosynthesis II: Ynk1 catalyses dADP + ATP -> dATP. NDPK activity is correct regardless of which pathway context generated the row. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0004550 nucleoside diphosphate kinase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways guanosine ribonucleotides de novo biosynthesis: Ynk1 catalyses GDP + ATP -> GTP. NDPK activity is correct regardless of which pathway context generated the row. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0004550 nucleoside diphosphate kinase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways guanosine deoxyribonucleotides de novo biosynthesis II: Ynk1 catalyses dGDP + ATP -> dGTP. NDPK activity is correct regardless of which pathway context generated the row. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0004550 nucleoside diphosphate kinase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways superpathway of pyrimidine ribonucleotides de novo biosynthesis: Ynk1 catalyses UDP + ATP -> UTP. NDPK activity is correct regardless of which pathway context generated the row. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0004550 nucleoside diphosphate kinase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways superpathway of purine biosynthesis and salvage pathways: Ynk1 catalyses GDP, dADP and dGDP phosphorylation. NDPK activity is correct regardless of which pathway context generated the row. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0004550 nucleoside diphosphate kinase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways de novo biosynthesis of pyrimidine ribonucleotides: Ynk1 catalyses UDP + ATP -> UTP. NDPK activity is correct regardless of which pathway context generated the row. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0004550 nucleoside diphosphate kinase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways de novo biosynthesis of pyrimidine deoxyribonucleotides: Ynk1 catalyses dCDP, dTDP and dUDP phosphorylation. NDPK activity is correct regardless of which pathway context generated the row. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0004550 nucleoside diphosphate kinase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways salvage pathways of pyrimidine ribonucleotides: Ynk1 catalyses CDP + ATP -> CTP. NDPK activity is correct regardless of which pathway context generated the row. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT cytoplasm for the NDK family; Ynk1 is predominantly cytoplasmic. Supporting Evidence: PMID:12472466 Ynk1p, synthesized as a single gene product, must therefore be partitioned between cytoplasm and mitochondrial IMS fractions file:yeast/YNK1/YNK1-uniprot.txt Note=Localizes predominantly to the cytoplasm. A small fraction is |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location mapping (cytoplasm); correct. Supporting Evidence: file:yeast/YNK1/YNK1-uniprot.txt Note=Localizes predominantly to the cytoplasm. A small fraction is |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: Ynk1 detected in the purified mitochondrial proteome; consistent with its IMS pool. Supporting Evidence: PMID:16823961 A total of 851 different proteins (PROMITO dataset) were identified by use of multidimensional LC-MS/MS 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:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT node PTN000142925 (seeded by NME4-like and Ynk1 data) gives mitochondrion; correct for the IMS pool of Ynk1. 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 | EXP PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: Mitochondrial proteome data used by SGD for IMS localisation; consistent with the dedicated IMS studies. Supporting Evidence: PMID:16823961 A total of 851 different proteins (PROMITO dataset) were identified by use of multidimensional LC-MS/MS 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 | EXP PMID:22984289 Intermembrane space proteome of yeast mitochondria. | ACCEPT | Summary: Vogtle et al. IMS proteome (Bax-induced release) identifies Ynk1 as an authentic IMS protein that GFP surveys had missed. Supporting Evidence: PMID:22984289 many of the known IMS proteins either were localized to the cytosol and/or the nucleus (e.g. Mic14, Mic17, Cox17, Adk1, Cyc1, Mdm35, Sod1, Ynk1, Cox19, Cox23) |
| GO:0005758 mitochondrial intermembrane space | IDA PMID:12472466 Nucleoside diphosphate kinase of Saccharomyces cerevisiae, Y... | ACCEPT | Summary: Submitochondrial fractionation shows a small fraction of Ynk1 NDPK activity in the IMS. 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 | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location mapping (mitochondrion intermembrane space); correct. Supporting Evidence: file:yeast/YNK1/YNK1-uniprot.txt Note=Localizes predominantly to the cytoplasm. A small fraction is 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 | IDA PMID:12472466 Nucleoside diphosphate kinase of Saccharomyces cerevisiae, Y... | ACCEPT | Summary: Amutha & Pain found most Ynk1 NDPK activity in the cytosolic fraction; main site of action. Supporting Evidence: PMID:12472466 Ynk1p, synthesized as a single gene product, must therefore be partitioned between cytoplasm and mitochondrial IMS fractions 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 | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways superpathway of purine nucleotides de novo biosynthesis II default cytosol compartment; correct for the bulk of Ynk1, though a small fraction is in the mitochondrial IMS. Supporting Evidence: PMID:12472466 Ynk1p, synthesized as a single gene product, must therefore be partitioned between cytoplasm and mitochondrial IMS fractions |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways de novo biosynthesis of purine nucleotides default cytosol compartment; correct for the bulk of Ynk1, though a small fraction is in the mitochondrial IMS. Supporting Evidence: PMID:12472466 Ynk1p, synthesized as a single gene product, must therefore be partitioned between cytoplasm and mitochondrial IMS fractions |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways superpathway of histidine, purine, and pyrimidine biosynthesis default cytosol compartment; correct for the bulk of Ynk1, though a small fraction is in the mitochondrial IMS. Supporting Evidence: PMID:12472466 Ynk1p, synthesized as a single gene product, must therefore be partitioned between cytoplasm and mitochondrial IMS fractions |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways superpathway of guanosine nucleotides de novo biosynthesis II default cytosol compartment; correct for the bulk of Ynk1, though a small fraction is in the mitochondrial IMS. Supporting Evidence: PMID:12472466 Ynk1p, synthesized as a single gene product, must therefore be partitioned between cytoplasm and mitochondrial IMS fractions |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways superpathway of adenosine nucleotides de novo biosynthesis II default cytosol compartment; correct for the bulk of Ynk1, though a small fraction is in the mitochondrial IMS. Supporting Evidence: PMID:12472466 Ynk1p, synthesized as a single gene product, must therefore be partitioned between cytoplasm and mitochondrial IMS fractions |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways UTP and CTP de novo biosynthesis default cytosol compartment; correct for the bulk of Ynk1, though a small fraction is in the mitochondrial IMS. Supporting Evidence: PMID:12472466 Ynk1p, synthesized as a single gene product, must therefore be partitioned between cytoplasm and mitochondrial IMS fractions |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways adenosine deoxyribonucleotides de novo biosynthesis II default cytosol compartment; correct for the bulk of Ynk1, though a small fraction is in the mitochondrial IMS. Supporting Evidence: PMID:12472466 Ynk1p, synthesized as a single gene product, must therefore be partitioned between cytoplasm and mitochondrial IMS fractions |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways guanosine ribonucleotides de novo biosynthesis default cytosol compartment; correct for the bulk of Ynk1, though a small fraction is in the mitochondrial IMS. Supporting Evidence: PMID:12472466 Ynk1p, synthesized as a single gene product, must therefore be partitioned between cytoplasm and mitochondrial IMS fractions |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways guanosine deoxyribonucleotides de novo biosynthesis II default cytosol compartment; correct for the bulk of Ynk1, though a small fraction is in the mitochondrial IMS. Supporting Evidence: PMID:12472466 Ynk1p, synthesized as a single gene product, must therefore be partitioned between cytoplasm and mitochondrial IMS fractions |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways superpathway of pyrimidine ribonucleotides de novo biosynthesis default cytosol compartment; correct for the bulk of Ynk1, though a small fraction is in the mitochondrial IMS. Supporting Evidence: PMID:12472466 Ynk1p, synthesized as a single gene product, must therefore be partitioned between cytoplasm and mitochondrial IMS fractions |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways superpathway of purine biosynthesis and salvage pathways default cytosol compartment; correct for the bulk of Ynk1, though a small fraction is in the mitochondrial IMS. Supporting Evidence: PMID:12472466 Ynk1p, synthesized as a single gene product, must therefore be partitioned between cytoplasm and mitochondrial IMS fractions |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways de novo biosynthesis of pyrimidine ribonucleotides default cytosol compartment; correct for the bulk of Ynk1, though a small fraction is in the mitochondrial IMS. Supporting Evidence: PMID:12472466 Ynk1p, synthesized as a single gene product, must therefore be partitioned between cytoplasm and mitochondrial IMS fractions |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways de novo biosynthesis of pyrimidine deoxyribonucleotides default cytosol compartment; correct for the bulk of Ynk1, though a small fraction is in the mitochondrial IMS. Supporting Evidence: PMID:12472466 Ynk1p, synthesized as a single gene product, must therefore be partitioned between cytoplasm and mitochondrial IMS fractions |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways salvage pathways of pyrimidine ribonucleotides default cytosol compartment; correct for the bulk of Ynk1, though a small fraction is in the mitochondrial IMS. Supporting Evidence: PMID:12472466 Ynk1p, synthesized as a single gene product, must therefore be partitioned between cytoplasm and mitochondrial IMS fractions |
| GO:0006164 purine nucleotide biosynthetic process | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways superpathway of purine nucleotides de novo biosynthesis II: Ynk1 makes GTP, dATP and dGTP from the diphosphates; purine nucleotide biosynthesis is correct as the context of these reactions. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'- |
| GO:0006164 purine nucleotide biosynthetic process | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways de novo biosynthesis of purine nucleotides: Ynk1 makes GTP, dATP and dGTP from the diphosphates; purine nucleotide biosynthesis is correct as the context of these reactions. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'- |
| GO:0006183 GTP biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro NDK mapping to GTP biosynthetic process; Ynk1 phosphorylates GDP, UDP and CDP (CDP and UDP among the preferred acceptors). Correct. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways UTP and CTP de novo biosynthesis (UDP -> UTP) mapped to 'de novo' pyrimidine nucleobase biosynthetic process. NDPK acts on nucleotides after ring synthesis; the right process is UTP biosynthesis. Reason: Nucleobase ring-synthesis term is wrong for an NDP kinase. Proposed replacements: UTP biosynthetic process Supporting Evidence: 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:0006207 'de novo' pyrimidine nucleobase biosynthetic process | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways de novo biosynthesis of pyrimidine ribonucleotides (UDP -> UTP) mapped to 'de novo' pyrimidine nucleobase biosynthetic process. NDPK acts on nucleotides after ring synthesis; the right process is UTP biosynthesis. Reason: Nucleobase ring-synthesis term is wrong for an NDP kinase. Proposed replacements: UTP biosynthetic process Supporting Evidence: 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:0006207 'de novo' pyrimidine nucleobase biosynthetic process | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways pyrimidine deoxyribonucleotide pathway (dCDP, dTDP, dUDP phosphorylation) was mapped to 'de novo' pyrimidine nucleobase biosynthetic process. NDPK does not build the pyrimidine ring; the reactions are dNTP synthesis. Reason: Nucleobase ring-synthesis term is wrong for an NDP kinase. Proposed replacements: deoxyribonucleoside triphosphate biosynthetic process Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'- |
| GO:0006228 UTP biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro NDK mapping to UTP biosynthetic process; Ynk1 phosphorylates GDP, UDP and CDP (CDP and UDP among the preferred acceptors). Correct. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0006241 CTP biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro NDK mapping to CTP biosynthetic process; Ynk1 phosphorylates GDP, UDP and CDP (CDP and UDP among the preferred acceptors). Correct. Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0006974 DNA damage response | IMP PMID:18983998 YNK1, the yeast homolog of human metastasis suppressor NM23,... | KEEP AS NON CORE | Summary: ynk1 deletion delays repair of UV- and etoposide-induced nuclear DNA damage and increases mutation rates. The mechanism is unknown (dNTP supply, or NM23-like exonuclease/histidine kinase activities proposed); Ynk1 is not a dedicated DNA-damage response component. Reason: Experimentally supported phenotype, but likely indirect relative to the core NDPK function. Supporting Evidence: PMID:18983998 Ablation of YNK1 delayed repair of UV- and etoposide-induced nuclear DNA damage by 3-6h PMID:18983998 which contains a single NM23 homolog, YNK1 |
| GO:0009142 nucleoside triphosphate biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference to nucleoside triphosphate biosynthetic process; this is the general physiological role of NDPK (making all NTPs/dNTPs other than ATP). Supporting Evidence: file:yeast/YNK1/YNK1-uniprot.txt FUNCTION: Major role in the synthesis of nucleoside triphosphates other PMID:1659321 The broad substrate specificity and kinetic data suggest that the enzyme is involved in both DNA and RNA metabolism |
| GO:0009142 nucleoside triphosphate biosynthetic process | IDA PMID:5793714 Kinetic studies of yeast nucleoside diphosphate kinase. | ACCEPT | Summary: Curated from the Garces & Cleland kinetic study to nucleoside triphosphate biosynthetic process; this is the general physiological role of NDPK (making all NTPs/dNTPs other than ATP). Supporting Evidence: PMID:5793714 Kinetic studies of yeast nucleoside diphosphate kinase file:yeast/YNK1/YNK1-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 to nucleoside triphosphate biosynthetic process; this is the general physiological role of NDPK (making all NTPs/dNTPs other than ATP). Supporting Evidence: file:yeast/YNK1/YNK1-uniprot.txt FUNCTION: Major role in the synthesis of nucleoside triphosphates other PMID:1659321 The broad substrate specificity and kinetic data suggest that the enzyme is involved in both DNA and RNA metabolism |
| GO:0009165 nucleotide biosynthetic process | RCA GO_REF:0000123 | MODIFY | Summary: Generic 'nucleotide biosynthetic process' from the PRPP-PWY-1 superpathway; true but uninformative. Reason: Superpathway-level term; the specific process is NTP/dNTP synthesis. Proposed replacements: nucleoside triphosphate biosynthetic process Supporting Evidence: file:yeast/YNK1/YNK1-uniprot.txt FUNCTION: Major role in the synthesis of nucleoside triphosphates other |
| GO:0009220 pyrimidine ribonucleotide biosynthetic process | RCA GO_REF:0000123 | ACCEPT | Summary: From the pyrimidine ribonucleotide de novo superpathway (UDP to UTP); UTP is a pyrimidine ribonucleotide, so correct. Supporting Evidence: 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:0010138 pyrimidine ribonucleotide salvage | RCA GO_REF:0000123 | KEEP AS NON CORE | Summary: YeastPathways salvage pathways of pyrimidine ribonucleotides (CDP -> CTP): Ynk1 phosphorylates salvaged CDP. Correct in context, but Ynk1 is a general NDPK rather than a salvage-specific enzyme. Reason: Pathway context of the general NDPK activity. Supporting Evidence: 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:0043101 purine-containing compound salvage | RCA GO_REF:0000123 | KEEP AS NON CORE | Summary: YeastPathways superpathway of purine biosynthesis and salvage: Ynk1 phosphorylates GDP/dADP/dGDP downstream of salvage. Correct in context, non-specific. Reason: Pathway context of the general NDPK activity. Supporting Evidence: 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:0046085 adenosine metabolic process | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways adenosine deoxyribonucleotides de novo biosynthesis II (Ynk1: dADP + ATP -> dATP) was mapped to 'adenosine metabolic process', which concerns the nucleoside adenosine. Ynk1 neither makes nor metabolises adenosine; the reaction belongs to dATP biosynthesis. Reason: Pathway-to-GO mapping names the wrong compound class (nucleoside instead of deoxynucleotide). Proposed replacements: dATP biosynthetic process Supporting Evidence: file:yeast/YNK1/YNK1-uniprot.txt Reaction=a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'- PMID:1659321 The broad substrate specificity and kinetic data suggest that the enzyme is involved in both DNA and RNA metabolism |
| GO:0046086 adenosine biosynthetic process | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways superpathway of adenosine nucleotides de novo biosynthesis II (Ynk1: dADP + ATP -> dATP) was mapped to 'adenosine biosynthetic process', which concerns the nucleoside adenosine. Ynk1 neither makes nor metabolises adenosine; the reaction belongs to dATP biosynthesis. Reason: Pathway-to-GO mapping names the wrong compound class (nucleoside instead of deoxynucleotide). Proposed replacements: dATP biosynthetic process Supporting Evidence: file:yeast/YNK1/YNK1-uniprot.txt Reaction=a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'- PMID:1659321 The broad substrate specificity and kinetic data suggest that the enzyme is involved in both DNA and RNA metabolism |
| GO:0106387 'de novo' GMP biosynthetic process | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways superpathway of guanosine nucleotides de novo biosynthesis II (Ynk1: GDP and dGDP phosphorylation) mapped to 'de novo' GMP biosynthetic process. GMP synthesis ends at Gua1; Ynk1 acts two phosphorylations later and is not part of GMP biosynthesis. Reason: Ynk1's reaction is downstream of GMP; the correct process is (d)GTP biosynthesis. Proposed replacements: GTP biosynthetic process Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0106387 'de novo' GMP biosynthetic process | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways guanosine ribonucleotides de novo biosynthesis (Ynk1: GDP + ATP -> GTP) mapped to 'de novo' GMP biosynthetic process. GMP synthesis ends at Gua1; Ynk1 acts two phosphorylations later and is not part of GMP biosynthesis. Reason: Ynk1's reaction is downstream of GMP; the correct process is (d)GTP biosynthesis. Proposed replacements: GTP biosynthetic process Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
| GO:0106387 'de novo' GMP biosynthetic process | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways guanosine deoxyribonucleotides de novo biosynthesis II (Ynk1: dGDP + ATP -> dGTP) mapped to 'de novo' GMP biosynthetic process. GMP synthesis ends at Gua1; Ynk1 acts two phosphorylations later and is not part of GMP biosynthesis. Reason: Ynk1's reaction is downstream of GMP; the correct process is (d)GTP biosynthesis. Proposed replacements: dGTP biosynthetic process Supporting Evidence: PMID:1659321 the relative activity of nucleoside diphosphates (NDP) as phosphate acceptors is in the order of dTDP greater than CDP greater than UDP file:yeast/YNK1/YNK1-uniprot.txt Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'- |
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Download this section (compressed HTML)Q: Which enzymes provide NDP kinase activity in ynk1 null cells (e.g. adenylate kinases or other NMP kinases), and how much of total NTP/dNTP synthesis does Ynk1 normally carry?
Q: Is the DNA-repair defect of ynk1 mutants due to altered dNTP pools or to an NM23-like non-NDPK activity of Ynk1?
Experiment: Measure NTP/dNTP pools and repair kinetics in ynk1 cells complemented with catalytically dead (active-site histidine) versus wild-type Ynk1.
Nucleoside diphosphate kinase; catalyzes the transfer of gamma phosphates from nucleoside triphosphates, usually ATP, to nucleoside diphosphates by a mechanism that involves formation of an autophosphorylated enzyme intermediate; protein abundance increases in response to DNA replication stress
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