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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: Annotation score: 3 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.

Catalytic activityi

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei12 – 121ATPBy similarity
Binding sitei60 – 601ATPBy similarity
Binding sitei88 – 881ATPBy similarity
Binding sitei94 – 941ATPBy similarity
Binding sitei105 – 1051ATPBy similarity
Binding sitei118 – 1181ATPBy similarity
Active sitei121 – 1211Pros-phosphohistidine intermediateBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Nucleotide metabolism

Keywords - Ligandi

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

Enzyme and pathway databases

BioCyciPHOR70601:GJWR-694-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoside diphosphate kinase (EC:2.7.4.6)
Short name:
NDK
Short name:
NDP kinase
Alternative name(s):
Nucleoside-2-P kinase
Gene namesi
Name:ndk
Ordered Locus Names:PH0698
OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Taxonomic identifieri70601 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000000752 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 157157Nucleoside diphosphate kinasePRO_0000137099Add
BLAST

Keywords - PTMi

Phosphoprotein

Interactioni

Protein-protein interaction databases

STRINGi70601.PH0698.

Structurei

Secondary structure

1
157
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 118Combined sources
Helixi13 – 175Combined sources
Helixi21 – 3111Combined sources
Beta strandi34 – 418Combined sources
Helixi45 – 517Combined sources
Helixi53 – 553Combined sources
Helixi61 – 688Combined sources
Beta strandi73 – 819Combined sources
Helixi83 – 919Combined sources
Helixi96 – 983Combined sources
Helixi104 – 1085Combined sources
Beta strandi113 – 1153Combined sources
Beta strandi119 – 1224Combined sources
Helixi126 – 13611Combined sources
Helixi139 – 1413Combined sources
Helixi150 – 1534Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 2-157.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO58429.

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.Curated

Phylogenomic databases

eggNOGiarCOG04313. Archaea.
COG0105. LUCA.
HOGENOMiHOG000224564.
KOiK00940.
OMAiAVGRNIC.

Family and domain databases

HAMAPiMF_00451. NDP_kinase. 1 hit.
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]
PROSITEiPS00469. NDP_KINASES. 1 hit.
[Graphical view]

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.

Cross-referencesi

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 2-157.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi70601.PH0698.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA29789; BAA29789; BAA29789.
GeneIDi1443028.
KEGGipho:PH0698.

Phylogenomic databases

eggNOGiarCOG04313. Archaea.
COG0105. LUCA.
HOGENOMiHOG000224564.
KOiK00940.
OMAiAVGRNIC.

Enzyme and pathway databases

BioCyciPHOR70601:GJWR-694-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO58429.

Family and domain databases

HAMAPiMF_00451. NDP_kinase. 1 hit.
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]
PROSITEiPS00469. NDP_KINASES. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNDK_PYRHO
AccessioniPrimary (citable) accession number: O58429
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: September 26, 2001
Last modified: November 11, 2015
This is version 97 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

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 one 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.