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P36010

- NDK_YEAST

UniProt

P36010 - NDK_YEAST

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Protein
Nucleoside diphosphate kinase
Gene
YNK1, NDK1, YNK, YKL067W, YKL333
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - 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.UniRule annotation

Cofactori

Magnesium By similarity.UniRule annotation

Kineticsi

  1. KM=25 µM for ADP2 Publications
  2. KM=300 µM for CDP
  3. KM=690 µM for UDP
  4. KM=400 µM for dCDP
  5. KM=220 µM for dGDP
  6. KM=370 µM for dTDP
  7. KM=530 µM for dUDP
  8. KM=220 µM for ATP
  9. KM=100 µM for CTP
  10. KM=150 µM for GTP
  11. KM=140 µM for UTP
  12. KM=170 µM for dCTP
  13. KM=22 µM for dGTP
  14. KM=110 µM for dTTP
  15. 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

Sites

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

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. identical protein binding Source: IntAct
  3. metal ion binding Source: UniProtKB-KW
  4. nucleoside diphosphate kinase activity Source: SGD
Complete GO annotation...

GO - Biological processi

  1. CTP biosynthetic process Source: InterPro
  2. DNA repair Source: UniProtKB-KW
  3. GTP biosynthetic process Source: InterPro
  4. UTP biosynthetic process Source: InterPro
  5. cellular response to DNA damage stimulus Source: SGD
  6. nucleoside diphosphate phosphorylation Source: SGD
  7. nucleoside triphosphate biosynthetic process Source: SGD
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.
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: Chromosome XI

Organism-specific databases

CYGDiYKL067w.
SGDiS000001550. YNK1.

Subcellular locationi

Cytoplasm. Mitochondrion intermembrane space
Note: Localizes predominantly to the cytoplasm. A small fraction is present in the mitochondrial intermembrane space.1 Publication

GO - Cellular componenti

  1. cytosol Source: SGD
  2. 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 kinaseUniRule annotation
PRO_0000137153Add
BLAST

Amino acid modifications

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

Post-translational modificationi

The N-terminus is blocked.UniRule annotation

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

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3B54X-ray3.10A/B1-153[»]
ProteinModelPortaliP36010.
SMRiP36010. Positions 2-153.

Miscellaneous databases

EvolutionaryTraceiP36010.

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.

Phylogenomic databases

eggNOGiCOG0105.
GeneTreeiENSGT00700000104244.
HOGENOMiHOG000224564.
KOiK00940.
OMAiARSHSIH.
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

MSSQTERTFI AVKPDGVQRG LVSQILSRFE KKGYKLVAIK LVKADDKLLE    50
QHYAEHVGKP FFPKMVSFMK SGPILATVWE GKDVVRQGRT ILGATNPLGS 100
APGTIRGDFG IDLGRNVCHG SDSVDSAERE INLWFKKEEL VDWESNQAKW 150
IYE 153
Length:153
Mass (Da):17,167
Last modified:June 1, 1994 - v1
Checksum:iBE37ACED90A44D00
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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 .
PIRi S37889.
RefSeqi NP_012856.1. NM_001179633.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3B54 X-ray 3.10 A/B 1-153 [» ]
ProteinModelPortali P36010.
SMRi P36010. Positions 2-153.
ModBasei Search...

Protein-protein interaction databases

BioGridi 34067. 41 interactions.
DIPi DIP-1969N.
IntActi P36010. 36 interactions.
MINTi MINT-402348.
STRINGi 4932.YKL067W.

2D gel databases

UCD-2DPAGE P36010.

Proteomic databases

MaxQBi P36010.
PaxDbi P36010.
PeptideAtlasi P36010.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YKL067W ; YKL067W ; YKL067W .
GeneIDi 853798.
KEGGi sce:YKL067W.

Organism-specific databases

CYGDi YKL067w.
SGDi S000001550. YNK1.

Phylogenomic databases

eggNOGi COG0105.
GeneTreei ENSGT00700000104244.
HOGENOMi HOG000224564.
KOi K00940.
OMAi ARSHSIH.
OrthoDBi EOG7J9W2D.

Enzyme and pathway databases

BioCyci MetaCyc:YKL067W-MONOMER.
YEAST:YKL067W-MONOMER.
SABIO-RK P36010.

Miscellaneous databases

EvolutionaryTracei P36010.
NextBioi 974942.
PROi P36010.

Gene expression databases

Genevestigatori P36010.

Family and domain databases

Gene3Di 3.30.70.141. 1 hit.
HAMAPi MF_00451. NDP_kinase.
InterProi IPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view ]
Pfami PF00334. NDK. 1 hit.
[Graphical view ]
PRINTSi PR01243. NUCDPKINASE.
SMARTi SM00562. NDK. 1 hit.
[Graphical view ]
SUPFAMi SSF54919. SSF54919. 1 hit.
PROSITEi PS00469. NDP_KINASES. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: May 14, 2014
This is version 128 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.

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

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