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Nucleoside diphosphate kinase (NDK) (NDP kinase) (EC 2.7.4.6)

 NDK_YEAST               Reviewed;         153 AA.
P36010; D6VXM0;
01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
01-JUN-1994, sequence version 1.
25-OCT-2017, entry version 158.
RecName: Full=Nucleoside diphosphate kinase;
Short=NDK;
Short=NDP kinase;
EC=2.7.4.6;
Name=YNK1; Synonyms=NDK1, YNK; OrderedLocusNames=YKL067W;
ORFNames=YKL333;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=SP1;
PubMed=8392963; DOI=10.1016/0378-1119(93)90710-K;
Fukuchi T., Nikawa J., Kimura N., Watanabe K.;
"Isolation, overexpression and disruption of a Saccharomyces
cerevisiae YNK gene encoding nucleoside diphosphate kinase.";
Gene 129:141-146(1993).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=8091863; DOI=10.1002/yea.320100009;
Rasmussen S.W.;
"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:S69-S74(1994).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=8196765; DOI=10.1038/369371a0;
Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V.,
Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M.,
Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L.,
Daignan-Fornier B., del Rey F., Dion C., Domdey H., Duesterhoeft A.,
Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H.,
Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L.,
Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M.,
Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H.,
Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J.,
Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H.,
Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J.,
Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S.,
Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F.,
Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R.,
Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W.,
Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M.,
Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C.,
Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H.,
Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L.,
van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C.,
Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G.,
Zimmermann J., Haasemann M., Becker I., Mewes H.-W.;
"Complete DNA sequence of yeast chromosome XI.";
Nature 369:371-378(1994).
[4]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[5]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=17322287; DOI=10.1101/gr.6037607;
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., 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.J.G., Bulyk M.L., Harlow E., Marsischky G.,
Kolodner R.D., LaBaer J.;
"Approaching a complete repository of sequence-verified protein-
encoding clones for Saccharomyces cerevisiae.";
Genome Res. 17:536-543(2007).
[6]
SUBUNIT.
PubMed=4576138;
Palmieri R., Yue R.H., Jacobs H.K., Maland L., Wu L., Kuby S.A.;
"Nucleoside triphosphate-nucleoside diphosphate transphosphorylase
(nucleoside diphosphokinase). 3. Subunit structure of the crystalline
enzyme from brewers' yeast.";
J. Biol. Chem. 248:4486-4499(1973).
[7]
BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
PubMed=1659321; DOI=10.1016/0003-9861(91)90129-7;
Jong A.Y., Ma J.J.;
"Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification,
characterization, and substrate specificity.";
Arch. Biochem. Biophys. 291:241-246(1991).
[8]
SUBCELLULAR LOCATION, AND INTERACTION WITH TOM40.
PubMed=12472466; DOI=10.1042/BJ20021415;
Amutha B., Pain D.;
"Nucleoside diphosphate kinase of Saccharomyces cerevisiae, Ynk1p:
localization to the mitochondrial intermembrane space.";
Biochem. J. 370:805-815(2003).
[9]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[10]
BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=16957983; DOI=10.1007/s10863-006-9045-y;
Jeudy S., Claverie J.-M., Abergel C.;
"The nucleoside diphosphate kinase from mimivirus: a peculiar affinity
for deoxypyrimidine nucleotides.";
J. Bioenerg. Biomembr. 38:247-254(2006).
[11]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-95, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[12]
FUNCTION.
PubMed=18983998; DOI=10.1016/j.mrfmmm.2008.09.015;
Yang M., Jarrett S.G., Craven R., Kaetzel D.M.;
"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(2009).
[13]
X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS).
PubMed=18607079; DOI=10.1107/S1744309108015212;
Wang H., Bao R., Jiang C., Yang Z., Zhou C.Z., Chen Y.;
"Structure of Ynk1 from the yeast Saccharomyces cerevisiae.";
Acta Crystallogr. F 64:572-576(2008).
-!- FUNCTION: Major 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. {ECO:0000269|PubMed:18983998}.
-!- CATALYTIC ACTIVITY: ATP + nucleoside diphosphate = ADP +
nucleoside triphosphate.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=25 uM for ADP {ECO:0000269|PubMed:1659321,
ECO:0000269|PubMed:16957983};
KM=300 uM for CDP {ECO:0000269|PubMed:1659321,
ECO:0000269|PubMed:16957983};
KM=690 uM for UDP {ECO:0000269|PubMed:1659321,
ECO:0000269|PubMed:16957983};
KM=400 uM for dCDP {ECO:0000269|PubMed:1659321,
ECO:0000269|PubMed:16957983};
KM=220 uM for dGDP {ECO:0000269|PubMed:1659321,
ECO:0000269|PubMed:16957983};
KM=370 uM for dTDP {ECO:0000269|PubMed:1659321,
ECO:0000269|PubMed:16957983};
KM=530 uM for dUDP {ECO:0000269|PubMed:1659321,
ECO:0000269|PubMed:16957983};
KM=220 uM for ATP {ECO:0000269|PubMed:1659321,
ECO:0000269|PubMed:16957983};
KM=100 uM for CTP {ECO:0000269|PubMed:1659321,
ECO:0000269|PubMed:16957983};
KM=150 uM for GTP {ECO:0000269|PubMed:1659321,
ECO:0000269|PubMed:16957983};
KM=140 uM for UTP {ECO:0000269|PubMed:1659321,
ECO:0000269|PubMed:16957983};
KM=170 uM for dCTP {ECO:0000269|PubMed:1659321,
ECO:0000269|PubMed:16957983};
KM=22 uM for dGTP {ECO:0000269|PubMed:1659321,
ECO:0000269|PubMed:16957983};
KM=110 uM for dTTP {ECO:0000269|PubMed:1659321,
ECO:0000269|PubMed:16957983};
KM=130 uM for dUTP {ECO:0000269|PubMed:1659321,
ECO:0000269|PubMed:16957983};
Vmax=130 umol/min/mg enzyme toward ADP
{ECO:0000269|PubMed:1659321, ECO:0000269|PubMed:16957983};
Vmax=220 umol/min/mg enzyme toward CDP
{ECO:0000269|PubMed:1659321, ECO:0000269|PubMed:16957983};
Vmax=400 umol/min/mg enzyme toward UDP
{ECO:0000269|PubMed:1659321, ECO:0000269|PubMed:16957983};
Vmax=380 umol/min/mg enzyme toward dCDP
{ECO:0000269|PubMed:1659321, ECO:0000269|PubMed:16957983};
Vmax=132 umol/min/mg enzyme toward dGDP
{ECO:0000269|PubMed:1659321, ECO:0000269|PubMed:16957983};
Vmax=330 umol/min/mg enzyme toward dTDP
{ECO:0000269|PubMed:1659321, ECO:0000269|PubMed:16957983};
Vmax=8.6 nmol/min/mg enzyme toward dUDP
{ECO:0000269|PubMed:1659321, ECO:0000269|PubMed:16957983};
Vmax=170 umol/min/mg enzyme toward ATP
{ECO:0000269|PubMed:1659321, ECO:0000269|PubMed:16957983};
Vmax=83 umol/min/mg enzyme toward CTP
{ECO:0000269|PubMed:1659321, ECO:0000269|PubMed:16957983};
Vmax=350 umol/min/mg enzyme toward GTP
{ECO:0000269|PubMed:1659321, ECO:0000269|PubMed:16957983};
Vmax=75 umol/min/mg enzyme toward UTP
{ECO:0000269|PubMed:1659321, ECO:0000269|PubMed:16957983};
Vmax=110 umol/min/mg enzyme toward dCTP
{ECO:0000269|PubMed:1659321, ECO:0000269|PubMed:16957983};
Vmax=38 umol/min/mg enzyme toward dGTP
{ECO:0000269|PubMed:1659321, ECO:0000269|PubMed:16957983};
Vmax=105 umol/min/mg enzyme toward dTTP
{ECO:0000269|PubMed:1659321, ECO:0000269|PubMed:16957983};
Vmax=90 umol/min/mg enzyme toward dUTP
{ECO:0000269|PubMed:1659321, ECO:0000269|PubMed:16957983};
-!- SUBUNIT: Homohexamer and homotetramer. Interacts with TOM40
preferentially in an unfolded, unphosphorylated form.
{ECO:0000269|PubMed:12472466, ECO:0000269|PubMed:1659321,
ECO:0000269|PubMed:4576138}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:12472466}.
Mitochondrion intermembrane space {ECO:0000269|PubMed:12472466}.
Note=Localizes predominantly to the cytoplasm. A small fraction is
present in the mitochondrial intermembrane space.
-!- PTM: The N-terminus is blocked.
-!- MISCELLANEOUS: Present with 7130 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the NDK family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; D13562; BAA02758.1; -; Genomic_DNA.
EMBL; X75780; CAA53407.1; -; Genomic_DNA.
EMBL; Z28067; CAA81904.1; -; Genomic_DNA.
EMBL; AY558263; AAS56589.1; -; Genomic_DNA.
EMBL; BK006944; DAA09090.1; -; Genomic_DNA.
PIR; S37889; S37889.
RefSeq; NP_012856.1; NM_001179633.1.
PDB; 3B54; X-ray; 3.10 A; A/B=1-153.
PDBsum; 3B54; -.
ProteinModelPortal; P36010; -.
SMR; P36010; -.
BioGrid; 34067; 114.
DIP; DIP-1969N; -.
IntAct; P36010; 37.
MINT; MINT-402348; -.
STRING; 4932.YKL067W; -.
iPTMnet; P36010; -.
UCD-2DPAGE; P36010; -.
MaxQB; P36010; -.
PRIDE; P36010; -.
EnsemblFungi; YKL067W; YKL067W; YKL067W.
GeneID; 853798; -.
KEGG; sce:YKL067W; -.
EuPathDB; FungiDB:YKL067W; -.
SGD; S000001550; YNK1.
GeneTree; ENSGT00760000119146; -.
HOGENOM; HOG000224564; -.
InParanoid; P36010; -.
KO; K00940; -.
OMA; KIVAMKM; -.
OrthoDB; EOG092C4PYA; -.
BioCyc; MetaCyc:YKL067W-MONOMER; -.
BioCyc; YEAST:YKL067W-MONOMER; -.
Reactome; R-SCE-499943; Interconversion of nucleotide di- and triphosphates.
Reactome; R-SCE-6798695; Neutrophil degranulation.
SABIO-RK; P36010; -.
EvolutionaryTrace; P36010; -.
PRO; PR:P36010; -.
Proteomes; UP000002311; Chromosome XI.
GO; GO:0005829; C:cytosol; IDA:SGD.
GO; GO:0005758; C:mitochondrial intermembrane space; IDA:SGD.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0004550; F:nucleoside diphosphate kinase activity; IDA:SGD.
GO; GO:0006974; P:cellular response to DNA damage stimulus; IMP:SGD.
GO; GO:0006241; P:CTP biosynthetic process; IEA:InterPro.
GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
GO; GO:0006183; P:GTP biosynthetic process; IEA:InterPro.
GO; GO:0006165; P:nucleoside diphosphate phosphorylation; IDA:SGD.
GO; GO:0009142; P:nucleoside triphosphate biosynthetic process; IDA:SGD.
GO; GO:0006228; P:UTP biosynthetic process; IEA:InterPro.
Gene3D; 3.30.70.141; -; 1.
HAMAP; MF_00451; NDP_kinase; 1.
InterPro; IPR034907; NDK-like_dom.
InterPro; IPR036850; NDK-like_dom_sf.
InterPro; IPR001564; Nucleoside_diP_kinase.
InterPro; IPR023005; Nucleoside_diP_kinase_AS.
Pfam; PF00334; NDK; 1.
PRINTS; PR01243; NUCDPKINASE.
SMART; SM00562; NDK; 1.
SUPFAM; SSF54919; SSF54919; 1.
PROSITE; PS00469; NDP_KINASES; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Complete proteome; Cytoplasm; DNA damage;
DNA repair; Kinase; Magnesium; Metal-binding; Mitochondrion;
Nucleotide metabolism; Nucleotide-binding; Phosphoprotein;
Reference proteome; Transferase.
CHAIN 1 153 Nucleoside diphosphate kinase.
/FTId=PRO_0000137153.
ACT_SITE 119 119 Pros-phosphohistidine intermediate.
{ECO:0000250}.
BINDING 13 13 ATP. {ECO:0000250}.
BINDING 61 61 ATP. {ECO:0000250}.
BINDING 89 89 ATP. {ECO:0000250}.
BINDING 95 95 ATP. {ECO:0000250}.
BINDING 106 106 ATP. {ECO:0000250}.
BINDING 116 116 ATP. {ECO:0000250}.
MOD_RES 95 95 Phosphothreonine.
{ECO:0000244|PubMed:18407956}.
STRAND 7 12 {ECO:0000244|PDB:3B54}.
HELIX 14 19 {ECO:0000244|PDB:3B54}.
HELIX 22 32 {ECO:0000244|PDB:3B54}.
STRAND 35 42 {ECO:0000244|PDB:3B54}.
HELIX 46 52 {ECO:0000244|PDB:3B54}.
HELIX 63 70 {ECO:0000244|PDB:3B54}.
STRAND 74 81 {ECO:0000244|PDB:3B54}.
HELIX 84 92 {ECO:0000244|PDB:3B54}.
HELIX 97 99 {ECO:0000244|PDB:3B54}.
HELIX 105 109 {ECO:0000244|PDB:3B54}.
STRAND 117 120 {ECO:0000244|PDB:3B54}.
HELIX 124 134 {ECO:0000244|PDB:3B54}.
HELIX 148 151 {ECO:0000244|PDB:3B54}.
SEQUENCE 153 AA; 17167 MW; BE37ACED90A44D00 CRC64;
MSSQTERTFI AVKPDGVQRG LVSQILSRFE KKGYKLVAIK LVKADDKLLE QHYAEHVGKP
FFPKMVSFMK SGPILATVWE GKDVVRQGRT ILGATNPLGS APGTIRGDFG IDLGRNVCHG
SDSVDSAERE INLWFKKEEL VDWESNQAKW IYE


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