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Protein

Nucleoside diphosphate kinase

Gene

ndk

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed-Annotation score: -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.UniRule annotation

Catalytic activityi

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.UniRule annotation

Cofactori

Mg2+UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei12ATPUniRule annotation1
Binding sitei60ATPUniRule annotation1
Binding sitei88ATPUniRule annotation1
Binding sitei94ATPUniRule annotation1
Binding sitei105ATPUniRule annotation1
Active sitei121Pros-phosphohistidine intermediateUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionKinase, Transferase
Biological processNucleotide metabolism
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciPHOR70601:G1G39-685-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoside diphosphate kinaseUniRule annotation (EC:2.7.4.6UniRule annotation)
Short name:
NDKUniRule annotation
Short name:
NDP kinaseUniRule annotation
Alternative name(s):
Nucleoside-2-P kinaseUniRule annotation
Gene namesi
Name:ndkUniRule annotation
Ordered Locus Names:PH0698
OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Taxonomic identifieri70601 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001370991 – 157Nucleoside diphosphate kinaseAdd BLAST157

Keywords - PTMi

Phosphoprotein

Interactioni

Protein-protein interaction databases

STRINGi70601.PH0698

Structurei

Secondary structure

1157
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 11Combined sources8
Helixi13 – 17Combined sources5
Helixi21 – 31Combined sources11
Beta strandi34 – 41Combined sources8
Helixi45 – 51Combined sources7
Helixi53 – 55Combined sources3
Helixi61 – 68Combined sources8
Beta strandi73 – 81Combined sources9
Helixi83 – 91Combined sources9
Helixi96 – 98Combined sources3
Helixi104 – 108Combined sources5
Beta strandi113 – 115Combined sources3
Beta strandi119 – 122Combined sources4
Helixi126 – 136Combined sources11
Helixi139 – 141Combined sources3
Helixi150 – 153Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2CWKX-ray1.75A/B1-157[»]
2DXDX-ray1.77A/B1-157[»]
2DXEX-ray1.70A/B1-157[»]
2DXFX-ray1.70A/B1-157[»]
2DY9X-ray2.01A/B1-157[»]
2DYAX-ray1.77A/B1-157[»]
ProteinModelPortaliO58429
SMRiO58429
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO58429

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.UniRule annotationCurated

Phylogenomic databases

eggNOGiarCOG04313 Archaea
COG0105 LUCA
HOGENOMiHOG000224564
KOiK00940
OMAiKIVAMKM
OrthoDBiPOG093Z0ECU

Family and domain databases

Gene3Di3.30.70.141, 1 hit
HAMAPiMF_00451 NDP_kinase, 1 hit
InterProiView protein in InterPro
IPR034907 NDK-like_dom
IPR036850 NDK-like_dom_sf
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.

O58429-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSETERTLVI IKPDAVVRGL IGEIISRFEK KGLKIVGMKM IWIDRELAEK
60 70 80 90 100
HYEEHREKPF FKALIDYITK TPVVVMVLEG RYAVEVVRKM AGATDPKDAA
110 120 130 140 150
PGTIRGDFGL EVSDAICNVI HASDSKESAE REISLFFKPE ELFEYPRAAD

WFYKKGI
Length:157
Mass (Da):17,908
Last modified:September 26, 2001 - v2
Checksum:i66D242C6BB46AAF5
GO

Sequence cautioni

The sequence BAA29789 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA Translation: BAA29789.1 Different initiation.
PIRiC71116
RefSeqiWP_048053198.1, NC_000961.1

Genome annotation databases

EnsemblBacteriaiBAA29789; BAA29789; BAA29789
GeneIDi1443028
KEGGipho:PH0698

Entry informationi

Entry nameiNDK_PYRHO
AccessioniPrimary (citable) accession number: O58429
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: September 26, 2001
Last modified: April 25, 2018
This is version 107 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic 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

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