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P36010 (NDK_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 127. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Nucleoside diphosphate kinase

Short name=NDK
Short name=NDP kinase
EC=2.7.4.6
Gene names
Name:YNK1
Synonyms:NDK1, YNK
Ordered Locus Names:YKL067W
ORF Names:YKL333
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length153 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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. Ref.12

Catalytic activity

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate. HAMAP-Rule MF_00451

Cofactor

Magnesium By similarity. HAMAP-Rule MF_00451

Subunit structure

Homohexamer and homotetramer. Interacts with TOM40 preferentially in an unfolded, unphosphorylated form. Ref.6 Ref.7 Ref.8

Subcellular location

Cytoplasm. Mitochondrion intermembrane space. Note: Localizes predominantly to the cytoplasm. A small fraction is present in the mitochondrial intermembrane space. Ref.8

Post-translational modification

The N-terminus is blocked. HAMAP-Rule MF_00451

Miscellaneous

Present with 7130 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the NDK family.

Biophysicochemical properties

Kinetic parameters:

KM=25 µM for ADP Ref.7 Ref.10

KM=300 µM for CDP

KM=690 µM for UDP

KM=400 µM for dCDP

KM=220 µM for dGDP

KM=370 µM for dTDP

KM=530 µM for dUDP

KM=220 µM for ATP

KM=100 µM for CTP

KM=150 µM for GTP

KM=140 µM for UTP

KM=170 µM for dCTP

KM=22 µM for dGTP

KM=110 µM for dTTP

KM=130 µM for dUTP

Vmax=130 µmol/min/mg enzyme toward ADP

Vmax=220 µmol/min/mg enzyme toward CDP

Vmax=400 µmol/min/mg enzyme toward UDP

Vmax=380 µmol/min/mg enzyme toward dCDP

Vmax=132 µmol/min/mg enzyme toward dGDP

Vmax=330 µmol/min/mg enzyme toward dTDP

Vmax=8.6 nmol/min/mg enzyme toward dUDP

Vmax=170 µmol/min/mg enzyme toward ATP

Vmax=83 µmol/min/mg enzyme toward CTP

Vmax=350 µmol/min/mg enzyme toward GTP

Vmax=75 µmol/min/mg enzyme toward UTP

Vmax=110 µmol/min/mg enzyme toward dCTP

Vmax=38 µmol/min/mg enzyme toward dGTP

Vmax=105 µmol/min/mg enzyme toward dTTP

Vmax=90 µmol/min/mg enzyme toward dUTP

Binary interactions

With

Entry

#Exp.

IntAct

Notes

itself3EBI-11968,EBI-11968

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 153153Nucleoside diphosphate kinase HAMAP-Rule MF_00451
PRO_0000137153

Sites

Active site1191Pros-phosphohistidine intermediate By similarity
Binding site131ATP By similarity
Binding site611ATP By similarity
Binding site891ATP By similarity
Binding site951ATP By similarity
Binding site1061ATP By similarity
Binding site1161ATP By similarity

Amino acid modifications

Modified residue951Phosphothreonine Ref.11

Secondary structure

........................... 153
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P36010 [UniParc].

Last modified June 1, 1994. Version 1.
Checksum: BE37ACED90A44D00

FASTA15317,167
        10         20         30         40         50         60 
MSSQTERTFI AVKPDGVQRG LVSQILSRFE KKGYKLVAIK LVKADDKLLE QHYAEHVGKP 

        70         80         90        100        110        120 
FFPKMVSFMK SGPILATVWE GKDVVRQGRT ILGATNPLGS APGTIRGDFG IDLGRNVCHG 

       130        140        150 
SDSVDSAERE INLWFKKEEL VDWESNQAKW IYE 

« Hide

References

« Hide 'large scale' references
[1]"Isolation, overexpression and disruption of a Saccharomyces cerevisiae YNK gene encoding nucleoside diphosphate kinase."
Fukuchi T., Nikawa J., Kimura N., Watanabe K.
Gene 129:141-146(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: SP1.
[2]"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."
Rasmussen S.W.
Yeast 10:S69-S74(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"Complete DNA sequence of yeast chromosome XI."
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. expand/collapse author list , 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.
Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[4]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[5]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
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. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[6]"Nucleoside triphosphate-nucleoside diphosphate transphosphorylase (nucleoside diphosphokinase). 3. Subunit structure of the crystalline enzyme from brewers' yeast."
Palmieri R., Yue R.H., Jacobs H.K., Maland L., Wu L., Kuby S.A.
J. Biol. Chem. 248:4486-4499(1973) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT.
[7]"Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity."
Jong A.Y., Ma J.J.
Arch. Biochem. Biophys. 291:241-246(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
[8]"Nucleoside diphosphate kinase of Saccharomyces cerevisiae, Ynk1p: localization to the mitochondrial intermembrane space."
Amutha B., Pain D.
Biochem. J. 370:805-815(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, INTERACTION WITH TOM40.
[9]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[10]"The nucleoside diphosphate kinase from mimivirus: a peculiar affinity for deoxypyrimidine nucleotides."
Jeudy S., Claverie J.-M., Abergel C.
J. Bioenerg. Biomembr. 38:247-254(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: BIOPHYSICOCHEMICAL PROPERTIES.
[11]"A multidimensional chromatography technology for in-depth phosphoproteome analysis."
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-95, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]"YNK1, the yeast homolog of human metastasis suppressor NM23, is required for repair of UV radiation- and etoposide-induced DNA damage."
Yang M., Jarrett S.G., Craven R., Kaetzel D.M.
Mutat. Res. 660:74-78(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[13]"Structure of Ynk1 from the yeast Saccharomyces cerevisiae."
Wang H., Bao R., Jiang C., Yang Z., Zhou C.Z., Chen Y.
Acta Crystallogr. F 64:572-576(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
D13562 Genomic DNA. Translation: BAA02758.1.
X75780 Genomic DNA. Translation: CAA53407.1.
Z28067 Genomic DNA. Translation: CAA81904.1.
AY558263 Genomic DNA. Translation: AAS56589.1.
BK006944 Genomic DNA. Translation: DAA09090.1.
PIRS37889.
RefSeqNP_012856.1. NM_001179633.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3B54X-ray3.10A/B1-153[»]
ProteinModelPortalP36010.
SMRP36010. Positions 2-153.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid34067. 41 interactions.
DIPDIP-1969N.
IntActP36010. 36 interactions.
MINTMINT-402348.
STRING4932.YKL067W.

2D gel databases

UCD-2DPAGEP36010.

Proteomic databases

PaxDbP36010.
PeptideAtlasP36010.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYKL067W; YKL067W; YKL067W.
GeneID853798.
KEGGsce:YKL067W.

Organism-specific databases

CYGDYKL067w.
SGDS000001550. YNK1.

Phylogenomic databases

eggNOGCOG0105.
GeneTreeENSGT00700000104244.
HOGENOMHOG000224564.
KOK00940.
OMAAEHSERP.
OrthoDBEOG7J9W2D.

Enzyme and pathway databases

BioCycMetaCyc:YKL067W-MONOMER.
YEAST:YKL067W-MONOMER.
SABIO-RKP36010.

Gene expression databases

GenevestigatorP36010.

Family and domain databases

Gene3D3.30.70.141. 1 hit.
HAMAPMF_00451. NDP_kinase.
InterProIPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]
PfamPF00334. NDK. 1 hit.
[Graphical view]
PRINTSPR01243. NUCDPKINASE.
SMARTSM00562. NDK. 1 hit.
[Graphical view]
SUPFAMSSF54919. SSF54919. 1 hit.
PROSITEPS00469. NDP_KINASES. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP36010.
NextBio974942.
PROP36010.

Entry information

Entry nameNDK_YEAST
AccessionPrimary (citable) accession number: P36010
Secondary accession number(s): D6VXM0
Entry history
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: April 16, 2014
This is version 127 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XI

Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references