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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

Miscellaneous

Present with 7130 molecules/cell in log phase SD medium.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)DescriptionActionsGraphical viewLength
Binding sitei13ATPBy similarity1
Binding sitei61ATPBy similarity1
Binding sitei89ATPBy similarity1
Binding sitei95ATPBy similarity1
Binding sitei106ATPBy similarity1
Binding sitei116ATPBy similarity1
Active sitei119Pros-phosphohistidine intermediateBy similarity1

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

Keywordsi

Molecular functionKinase, Transferase
Biological processDNA damage, DNA repair, Nucleotide metabolism
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:YKL067W-MONOMER.
YEAST:YKL067W-MONOMER.
ReactomeiR-SCE-499943. Interconversion of nucleotide di- and triphosphates.
R-SCE-6798695. Neutrophil degranulation.
SABIO-RKiP36010.

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
Proteomesi
  • UP000002311 Componenti: Chromosome XI

Organism-specific databases

EuPathDBiFungiDB:YKL067W.
SGDiS000001550. YNK1.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001371531 – 153Nucleoside diphosphate kinaseAdd BLAST153

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei95PhosphothreonineCombined sources1

Post-translational modificationi

The N-terminus is blocked.

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP36010.
PRIDEiP36010.

2D gel databases

UCD-2DPAGEiP36010.

PTM databases

iPTMnetiP36010.

Interactioni

Subunit structurei

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

Binary interactionsi

WithEntry#Exp.IntActNotes
itself4EBI-11968,EBI-11968

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi34067. 114 interactors.
DIPiDIP-1969N.
IntActiP36010. 39 interactors.
MINTiMINT-402348.
STRINGi4932.YKL067W.

Structurei

Secondary structure

1153
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi7 – 12Combined sources6
Helixi14 – 19Combined sources6
Helixi22 – 32Combined sources11
Beta strandi35 – 42Combined sources8
Helixi46 – 52Combined sources7
Helixi63 – 70Combined sources8
Beta strandi74 – 81Combined sources8
Helixi84 – 92Combined sources9
Helixi97 – 99Combined sources3
Helixi105 – 109Combined sources5
Beta strandi117 – 120Combined sources4
Helixi124 – 134Combined sources11
Helixi148 – 151Combined sources4

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP36010.

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.Curated

Phylogenomic databases

GeneTreeiENSGT00760000119146.
HOGENOMiHOG000224564.
InParanoidiP36010.
KOiK00940.
OMAiKIVAMKM.
OrthoDBiEOG092C4PYA.

Family and domain databases

Gene3Di3.30.70.141. 1 hit.
HAMAPiMF_00451. NDP_kinase. 1 hit.
InterProiView protein in InterPro
IPR034907. NDK-like_dom.
IPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
PfamiView protein in Pfam
PF00334. NDK. 1 hit.
PRINTSiPR01243. NUCDPKINASE.
SMARTiView protein in SMART
SM00562. NDK. 1 hit.
SUPFAMiSSF54919. SSF54919. 1 hit.
PROSITEiView protein in PROSITE
PS00469. NDP_KINASES. 1 hit.

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.

Similar proteinsi

Entry informationi

Entry nameiNDK_YEAST
AccessioniPrimary (citable) accession number: P36010
Secondary accession number(s): D6VXM0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: September 27, 2017
This is version 157 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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