Nucleoside diphosphate kinase - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P36010 (NDK_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 119. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended 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

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	153 AA.
Sequence status	Complete.
Protein existence	Evidence 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.
Cofactor	Magnesium By similarity.
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.
Miscellaneous	Present with 7130 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the NDK family.
Biophysicochemical properties	Kinetic parameters: K_M=25 µM for ADP Ref.7 Ref.10 K_M=300 µM for CDP K_M=690 µM for UDP K_M=400 µM for dCDP K_M=220 µM for dGDP K_M=370 µM for dTDP K_M=530 µM for dUDP K_M=220 µM for ATP K_M=100 µM for CTP K_M=150 µM for GTP K_M=140 µM for UTP K_M=170 µM for dCTP K_M=22 µM for dGTP K_M=110 µM for dTTP K_M=130 µM for dUTP V_max=130 µmol/min/mg enzyme toward ADP V_max=220 µmol/min/mg enzyme toward CDP V_max=400 µmol/min/mg enzyme toward UDP V_max=380 µmol/min/mg enzyme toward dCDP V_max=132 µmol/min/mg enzyme toward dGDP V_max=330 µmol/min/mg enzyme toward dTDP V_max=8.6 nmol/min/mg enzyme toward dUDP V_max=170 µmol/min/mg enzyme toward ATP V_max=83 µmol/min/mg enzyme toward CTP V_max=350 µmol/min/mg enzyme toward GTP V_max=75 µmol/min/mg enzyme toward UTP V_max=110 µmol/min/mg enzyme toward dCTP V_max=38 µmol/min/mg enzyme toward dGTP V_max=105 µmol/min/mg enzyme toward dTTP V_max=90 µmol/min/mg enzyme toward dUTP

Ontologies

Keywords
Biological process	DNA damage DNA repair Nucleotide metabolism
Cellular component	Cytoplasm Mitochondrion
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Kinase Transferase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	CTP biosynthetic process Inferred from electronic annotation. Source: InterPro DNA repair Inferred from electronic annotation. Source: UniProtKB-KW GTP biosynthetic process Inferred from electronic annotation. Source: InterPro UTP biosynthetic process Inferred from electronic annotation. Source: InterPro nucleoside triphosphate biosynthetic process Inferred from direct assay Ref.7. Source: SGD response to DNA damage stimulus Inferred from mutant phenotype Ref.12. Source: SGD
Cellular_component	cytosol Inferred from direct assay Ref.8. Source: SGD mitochondrial intermembrane space Inferred from direct assay Ref.8. Source: SGD
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleoside diphosphate kinase activity Inferred from direct assay Ref.8. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		3	EBI-11968,EBI-11968

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 153

153

Nucleoside diphosphate kinase

PRO_0000137153

Sites

Active site

119

Pros-phosphohistidine intermediate By similarity

Binding site

ATP By similarity

Binding site

ATP By similarity

Binding site

ATP By similarity

Binding site

ATP By similarity

Binding site

106

ATP By similarity

Binding site

116

ATP By similarity

Amino acid modifications

Modified residue

Phosphothreonine Ref.11

Secondary structure

153

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P36010 [UniParc].

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

FASTA

153

17,167

        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' referencesShow '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. 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. 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, MASS SPECTROMETRY.
[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.

PIR

S37889.

RefSeq

NP_012856.1. NM_001179633.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3B54	X-ray	3.10	A/B	1-153	[»]

ProteinModelPortal

P36010.

SMR

P36010. Positions 2-153.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1969N.

IntAct

P36010. 39 interactions.

MINT

MINT-402348.

STRING

4932.YKL067W.

2D gel databases

UCD-2DPAGE

P36010.

Proteomic databases

PaxDb

P36010.

PeptideAtlas

P36010.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YKL067W; YKL067W; YKL067W.

GeneID

853798.

KEGG

sce:YKL067W.

Organism-specific databases

CYGD

YKL067w.

SGD

S000001550. YNK1.

Phylogenomic databases

eggNOG

COG0105.

GeneTree

ENSGT00700000104244.

HOGENOM

HOG000224564.

K00940.

OMA

FRVVAMK.

OrthoDB

EOG470XSR.

Enzyme and pathway databases

SABIO-RK

P36010.

Gene expression databases

Genevestigator

P36010.

GermOnline

YKL067W. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

3.30.70.141. 1 hit.

InterPro

IPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]

PANTHER

PTHR11349. PTHR11349. 1 hit.

Pfam

PF00334. NDK. 1 hit.
[Graphical view]

PRINTS

PR01243. NUCDPKINASE.

SMART

SM00562. NDK. 1 hit.
[Graphical view]

SUPFAM

SSF54919. NDK. 1 hit.

PROSITE

PS00469. NDP_KINASES. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P36010.

NextBio

974942.

Entry information

Entry name

NDK_YEAST

Accession

Primary (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 3, 2013
This is version 119 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

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

Yeast chromosome XI

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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Sites

Amino acid modifications

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents