Nucleoside diphosphate kinase (P36010)

Identification
NameNucleoside diphosphate kinase
Synonyms
  • NDK
  • NDP kinase
Gene NameYNK1
Enzyme Class
Biological Properties
General FunctionInvolved in nucleoside diphosphate kinase activity
Specific FunctionMajor role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Required for repair of UV radiation- and etoposide-induced DNA damage
Cellular LocationCytoplasm. Mitochondrion intermembrane space.
SMPDB Pathways
Pyrimidine metabolismPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Purine metabolismec00230 Map00230
Pyrimidine metabolismec00240 Map00240
SMPDB ReactionsNot Available
KEGG Reactions
Adenosine triphosphate + dUDP ↔ Deoxyuridine triphosphate + ADP
Adenosine triphosphate + Guanosine diphosphate ↔ GTP + ADP
IDP + Adenosine triphosphate ↔ ITP + ADP
Adenosine triphosphate + Uridine 5'-diphosphate ↔ Uridine triphosphate + ADP
Metabolites
YMDB IDNameView
YMDB00064CDPShow
YMDB00109Adenosine triphosphateShow
YMDB00201Deoxyuridine triphosphateShow
YMDB00205dTDPShow
YMDB00257Guanosine diphosphateShow
YMDB00279Cytidine triphosphateShow
YMDB00307Uridine 5'-diphosphateShow
YMDB00326Uridine triphosphateShow
YMDB00558GTPShow
YMDB00559ITPShow
YMDB00658dCTPShow
YMDB00700dATPShow
YMDB00744dGTPShow
YMDB00745dTTPShow
YMDB00746dUDPShow
YMDB00898dGDPShow
YMDB00901dADPShow
YMDB00910IDPShow
YMDB00914ADPShow
YMDB00916dCDPShow
GO Classification
Component
Not Available
Function
ATP binding
transferase activity, transferring phosphorus-containing groups
phosphotransferase activity, phosphate group as acceptor
nucleoside diphosphate kinase activity
binding
nucleoside binding
purine nucleoside binding
adenyl nucleotide binding
catalytic activity
adenyl ribonucleotide binding
transferase activity
Process
metabolic process
pyrimidine nucleotide metabolic process
pyrimidine nucleotide biosynthetic process
nitrogen compound metabolic process
purine nucleoside triphosphate biosynthetic process
cellular nitrogen compound metabolic process
purine ribonucleoside triphosphate biosynthetic process
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
nucleobase, nucleoside and nucleotide metabolic process
nucleoside phosphate metabolic process
nucleotide metabolic process
CTP biosynthetic process
purine nucleotide metabolic process
pyrimidine nucleoside triphosphate biosynthetic process
purine nucleotide biosynthetic process
pyrimidine ribonucleoside triphosphate biosynthetic process
UTP biosynthetic process
GTP biosynthetic process
Gene Properties
Chromosome Locationchromosome 11
LocusYKL067W
Gene Sequence>462 bp ATGTCTAGTCAAACAGAAAGAACTTTTATTGCGGTAAAACCAGATGGTGTCCAGAGGGGC TTAGTATCTCAAATTCTATCTCGTTTTGAAAAAAAAGGTTACAAACTAGTTGCTATTAAA TTAGTTAAAGCGGATGATAAATTACTAGAGCAACATTACGCAGAGCATGTTGGTAAACCA TTTTTCCCAAAGATGGTATCCTTTATGAAGTCTGGTCCCATTTTGGCCACGGTCTGGGAG GGAAAAGATGTGGTTAGACAAGGAAGAACTATTCTTGGTGCTACTAATCCTTTGGGCAGT GCACCAGGTACCATTAGAGGTGATTTCGGTATTGACCTAGGCAGAAACGTCTGTCACGGC AGTGATTCTGTTGATAGCGCTGAACGTGAAATCAATTTGTGGTTTAAGAAGGAAGAGTTA GTTGATTGGGAATCTAATCAAGCTAAGTGGATTTATGAATGA
Protein Properties
Pfam Domain Function
Protein Residues153
Protein Molecular Weight17166.59961
Protein Theoretical pI9.05
Signalling Regions
  • None
Transmembrane Regions
  • None
Protein Sequence>Nucleoside diphosphate kinase MSSQTERTFIAVKPDGVQRGLVSQILSRFEKKGYKLVAIKLVKADDKLLEQHYAEHVGKP FFPKMVSFMKSGPILATVWEGKDVVRQGRTILGATNPLGSAPGTIRGDFGIDLGRNVCHG SDSVDSAEREINLWFKKEELVDWESNQAKWIYE
References
External Links
ResourceLink
Saccharomyces Genome Database YNK1
Uniprot IDP36010
Uniprot NameNDK_YEAST
GenBank Gene IDAY558263
Genebank Protein ID45270416
General Reference
  • Fukuchi, T., Nikawa, J., Kimura, N., Watanabe, K. (1993). "Isolation, overexpression and disruption of a Saccharomyces cerevisiae YNK gene encoding nucleoside diphosphate kinase." Gene 129:141-146.8392963
  • Rasmussen, S. W. (1994). "Sequence of a 20.7 kb region of yeast chromosome XI includes the NUP100 gene, an open reading frame (ORF) possibly representing a nucleoside diphosphate kinase gene, tRNAs for His, Val and Trp in addition to seven ORFs with weak or no significant similarity to known proteins." Yeast 10 Suppl A:S69-S74.8091863
  • Dujon, B., Alexandraki, D., Andre, B., Ansorge, W., Baladron, V., Ballesta, J. P., Banrevi, A., Bolle, P. A., Bolotin-Fukuhara, M., Bossier, P., et, a. l. .. (1994). "Complete DNA sequence of yeast chromosome XI." Nature 369:371-378.8196765
  • Hu, Y., Rolfs, A., Bhullar, B., Murthy, T. V., Zhu, C., Berger, M. F., Camargo, A. A., Kelley, F., McCarron, S., Jepson, D., Richardson, A., Raphael, J., Moreira, D., Taycher, E., Zuo, D., Mohr, S., Kane, M. F., Williamson, J., Simpson, A., Bulyk, M. L., Harlow, E., Marsischky, G., Kolodner, R. D., LaBaer, J. (2007). "Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Genome Res 17:536-543.17322287
  • Palmieri, R., Yue, R. H., Jacobs, H. K., Maland, L., Wu, L., Kuby, S. A. (1973). "Nucleoside triphosphate-nucleoside diphosphate transphosphorylase (nucleoside diphosphokinase). 3. Subunit structure of the crystalline enzyme from brewers' yeast." J Biol Chem 248:4486-4499.4576138
  • Jong, A. Y., Ma, J. J. (1991). "Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity." Arch Biochem Biophys 291:241-246.1659321
  • Amutha, B., Pain, D. (2003). "Nucleoside diphosphate kinase of Saccharomyces cerevisiae, Ynk1p: localization to the mitochondrial intermembrane space." Biochem J 370:805-815.12472466
  • Ghaemmaghami, S., Huh, W. K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., Weissman, J. S. (2003). "Global analysis of protein expression in yeast." Nature 425:737-741.14562106
  • Jeudy, S., Claverie, J. M., Abergel, C. (2006). "The nucleoside diphosphate kinase from mimivirus: a peculiar affinity for deoxypyrimidine nucleotides." J Bioenerg Biomembr 38:247-254.16957983
  • Albuquerque, C. P., Smolka, M. B., Payne, S. H., Bafna, V., Eng, J., Zhou, H. (2008). "A multidimensional chromatography technology for in-depth phosphoproteome analysis." Mol Cell Proteomics 7:1389-1396.18407956
  • Yang, M., Jarrett, S. G., Craven, R., Kaetzel, D. M. (2009). "YNK1, the yeast homolog of human metastasis suppressor NM23, is required for repair of UV radiation- and etoposide-induced DNA damage." Mutat Res 660:74-78.18983998
  • Wang, H., Bao, R., Jiang, C., Yang, Z., Zhou, C. Z., Chen, Y. (2008). "Structure of Ynk1 from the yeast Saccharomyces cerevisiae." Acta Crystallogr Sect F Struct Biol Cryst Commun 64:572-576.18607079