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Protein

Nucleoside diphosphate kinase

Gene

YNK1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.1 Publication

Catalytic activityi

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.

Cofactori

Mg2+By similarity

Kineticsi

  1. KM=25 µM for ADP2 Publications
  2. KM=300 µM for CDP2 Publications
  3. KM=690 µM for UDP2 Publications
  4. KM=400 µM for dCDP2 Publications
  5. KM=220 µM for dGDP2 Publications
  6. KM=370 µM for dTDP2 Publications
  7. KM=530 µM for dUDP2 Publications
  8. KM=220 µM for ATP2 Publications
  9. KM=100 µM for CTP2 Publications
  10. KM=150 µM for GTP2 Publications
  11. KM=140 µM for UTP2 Publications
  12. KM=170 µM for dCTP2 Publications
  13. KM=22 µM for dGTP2 Publications
  14. KM=110 µM for dTTP2 Publications
  15. KM=130 µM for dUTP2 Publications
  1. Vmax=130 µmol/min/mg enzyme toward ADP2 Publications
  2. Vmax=220 µmol/min/mg enzyme toward CDP2 Publications
  3. Vmax=400 µmol/min/mg enzyme toward UDP2 Publications
  4. Vmax=380 µmol/min/mg enzyme toward dCDP2 Publications
  5. Vmax=132 µmol/min/mg enzyme toward dGDP2 Publications
  6. Vmax=330 µmol/min/mg enzyme toward dTDP2 Publications
  7. Vmax=8.6 nmol/min/mg enzyme toward dUDP2 Publications
  8. Vmax=170 µmol/min/mg enzyme toward ATP2 Publications
  9. Vmax=83 µmol/min/mg enzyme toward CTP2 Publications
  10. Vmax=350 µmol/min/mg enzyme toward GTP2 Publications
  11. Vmax=75 µmol/min/mg enzyme toward UTP2 Publications
  12. Vmax=110 µmol/min/mg enzyme toward dCTP2 Publications
  13. Vmax=38 µmol/min/mg enzyme toward dGTP2 Publications
  14. Vmax=105 µmol/min/mg enzyme toward dTTP2 Publications
  15. Vmax=90 µmol/min/mg enzyme toward dUTP2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei13 – 131ATPBy similarity
Binding sitei61 – 611ATPBy similarity
Binding sitei89 – 891ATPBy similarity
Binding sitei95 – 951ATPBy similarity
Binding sitei106 – 1061ATPBy similarity
Binding sitei116 – 1161ATPBy similarity
Active sitei119 – 1191Pros-phosphohistidine intermediateBy similarity

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • identical protein binding Source: IntAct
  • metal ion binding Source: UniProtKB-KW
  • nucleoside diphosphate kinase activity Source: SGD

GO - Biological processi

  • cellular response to DNA damage stimulus Source: SGD
  • CTP biosynthetic process Source: InterPro
  • DNA repair Source: UniProtKB-KW
  • GTP biosynthetic process Source: InterPro
  • nucleoside diphosphate phosphorylation Source: SGD
  • nucleoside triphosphate biosynthetic process Source: SGD
  • UTP biosynthetic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

DNA damage, DNA repair, Nucleotide metabolism

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:YKL067W-MONOMER.
YEAST:YKL067W-MONOMER.
ReactomeiREACT_275578. Synthesis and interconversion of nucleotide di- and triphosphates.
SABIO-RKP36010.

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoside diphosphate kinase (EC:2.7.4.6)
Short name:
NDK
Short name:
NDP kinase
Gene namesi
Name:YNK1
Synonyms:NDK1, YNK
Ordered Locus Names:YKL067W
ORF Names:YKL333
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome XI

Organism-specific databases

CYGDiYKL067w.
EuPathDBiFungiDB:YKL067W.
SGDiS000001550. YNK1.

Subcellular locationi

  • Cytoplasm 1 Publication
  • Mitochondrion intermembrane space 1 Publication

  • Note: Localizes predominantly to the cytoplasm. A small fraction is present in the mitochondrial intermembrane space.

GO - Cellular componenti

  • cytosol Source: SGD
  • mitochondrial intermembrane space Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 153153Nucleoside diphosphate kinasePRO_0000137153Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei95 – 951Phosphothreonine1 Publication

Post-translational modificationi

The N-terminus is blocked.

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP36010.
PaxDbiP36010.
PeptideAtlasiP36010.

2D gel databases

UCD-2DPAGEP36010.

Expressioni

Gene expression databases

GenevestigatoriP36010.

Interactioni

Subunit structurei

Homohexamer and homotetramer. Interacts with TOM40 preferentially in an unfolded, unphosphorylated form.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself3EBI-11968,EBI-11968

Protein-protein interaction databases

BioGridi34067. 42 interactions.
DIPiDIP-1969N.
IntActiP36010. 36 interactions.
MINTiMINT-402348.
STRINGi4932.YKL067W.

Structurei

Secondary structure

1
153
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi7 – 126Combined sources
Helixi14 – 196Combined sources
Helixi22 – 3211Combined sources
Beta strandi35 – 428Combined sources
Helixi46 – 527Combined sources
Helixi63 – 708Combined sources
Beta strandi74 – 818Combined sources
Helixi84 – 929Combined sources
Helixi97 – 993Combined sources
Helixi105 – 1095Combined sources
Beta strandi117 – 1204Combined sources
Helixi124 – 13411Combined sources
Helixi148 – 1514Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3B54X-ray3.10A/B1-153[»]
ProteinModelPortaliP36010.
SMRiP36010. Positions 2-153.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP36010.

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.Curated

Phylogenomic databases

eggNOGiCOG0105.
GeneTreeiENSGT00760000119146.
HOGENOMiHOG000224564.
InParanoidiP36010.
KOiK00940.
OMAiFWFKADE.
OrthoDBiEOG7J9W2D.

Family and domain databases

Gene3Di3.30.70.141. 1 hit.
HAMAPiMF_00451. NDP_kinase.
InterProiIPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]
PfamiPF00334. NDK. 1 hit.
[Graphical view]
PRINTSiPR01243. NUCDPKINASE.
SMARTiSM00562. NDK. 1 hit.
[Graphical view]
SUPFAMiSSF54919. SSF54919. 1 hit.
PROSITEiPS00469. NDP_KINASES. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P36010-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSQTERTFI AVKPDGVQRG LVSQILSRFE KKGYKLVAIK LVKADDKLLE
60 70 80 90 100
QHYAEHVGKP FFPKMVSFMK SGPILATVWE GKDVVRQGRT ILGATNPLGS
110 120 130 140 150
APGTIRGDFG IDLGRNVCHG SDSVDSAERE INLWFKKEEL VDWESNQAKW

IYE
Length:153
Mass (Da):17,167
Last modified:June 1, 1994 - v1
Checksum:iBE37ACED90A44D00
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiS37889.
RefSeqiNP_012856.1. NM_001179633.1.

Genome annotation databases

EnsemblFungiiYKL067W; YKL067W; YKL067W.
GeneIDi853798.
KEGGisce:YKL067W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiS37889.
RefSeqiNP_012856.1. NM_001179633.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3B54X-ray3.10A/B1-153[»]
ProteinModelPortaliP36010.
SMRiP36010. Positions 2-153.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34067. 42 interactions.
DIPiDIP-1969N.
IntActiP36010. 36 interactions.
MINTiMINT-402348.
STRINGi4932.YKL067W.

2D gel databases

UCD-2DPAGEP36010.

Proteomic databases

MaxQBiP36010.
PaxDbiP36010.
PeptideAtlasiP36010.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYKL067W; YKL067W; YKL067W.
GeneIDi853798.
KEGGisce:YKL067W.

Organism-specific databases

CYGDiYKL067w.
EuPathDBiFungiDB:YKL067W.
SGDiS000001550. YNK1.

Phylogenomic databases

eggNOGiCOG0105.
GeneTreeiENSGT00760000119146.
HOGENOMiHOG000224564.
InParanoidiP36010.
KOiK00940.
OMAiFWFKADE.
OrthoDBiEOG7J9W2D.

Enzyme and pathway databases

BioCyciMetaCyc:YKL067W-MONOMER.
YEAST:YKL067W-MONOMER.
ReactomeiREACT_275578. Synthesis and interconversion of nucleotide di- and triphosphates.
SABIO-RKP36010.

Miscellaneous databases

EvolutionaryTraceiP36010.
NextBioi974942.
PROiP36010.

Gene expression databases

GenevestigatoriP36010.

Family and domain databases

Gene3Di3.30.70.141. 1 hit.
HAMAPiMF_00451. NDP_kinase.
InterProiIPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]
PfamiPF00334. NDK. 1 hit.
[Graphical view]
PRINTSiPR01243. NUCDPKINASE.
SMARTiSM00562. NDK. 1 hit.
[Graphical view]
SUPFAMiSSF54919. SSF54919. 1 hit.
PROSITEiPS00469. NDP_KINASES. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. 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. 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).

Entry informationi

Entry nameiNDK_YEAST
AccessioniPrimary (citable) accession number: P36010
Secondary accession number(s): D6VXM0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: April 29, 2015
This is version 134 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 7130 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XI
    Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.