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Protein

Nucleoside diphosphate kinase

Gene

ndk

Organism
Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halobacterium halobium)
Status
Reviewed-Annotation score: Annotation score: 4 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.UniRule annotation

Cofactori

Mg2+UniRule annotation

Sites

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

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

BioCyciMetaCyc:MONOMER-15776.
BRENDAi2.7.4.6. 2552.

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:VNG_1160G
OrganismiHalobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halobacterium halobium)
Taxonomic identifieri64091 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaHalobacteriaHalobacterialesHalobacteriaceaeHalobacterium
Proteomesi
  • UP000000554 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 161161Nucleoside diphosphate kinasePRO_0000137089Add
BLAST

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP61136.
PRIDEiP61136.

Interactioni

Protein-protein interaction databases

STRINGi64091.VNG1160G.

Structurei

Secondary structure

1
161
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi7 – 126Combined sources
Helixi14 – 185Combined sources
Helixi22 – 3110Combined sources
Beta strandi35 – 428Combined sources
Helixi46 – 527Combined sources
Helixi54 – 563Combined sources
Helixi62 – 698Combined sources
Beta strandi74 – 818Combined sources
Helixi84 – 929Combined sources
Helixi97 – 993Combined sources
Helixi105 – 1095Combined sources
Beta strandi113 – 1153Combined sources
Beta strandi117 – 1204Combined sources
Helixi128 – 1369Combined sources
Helixi139 – 1413Combined sources
Helixi150 – 1534Combined sources
Helixi155 – 1573Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2AZ1X-ray2.35A/B/C/D/E/F1-161[»]
2AZ3X-ray2.20A/B/C/D/E/F/G/H/I1-161[»]
ProteinModelPortaliP61136.
SMRiP61136. Positions 4-158.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP61136.

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.UniRule annotation

Phylogenomic databases

eggNOGiarCOG04313. Archaea.
COG0105. LUCA.
InParanoidiP61136.
KOiK00940.
OMAiVERFFME.
PhylomeDBiP61136.

Family and domain databases

HAMAPiMF_00451. NDP_kinase.
InterProiIPR001564. Nucleoside_diP_kinase.
[Graphical view]
PfamiPF00334. NDK. 1 hit.
[Graphical view]
PRINTSiPR01243. NUCDPKINASE.
SMARTiSM00562. NDK. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P61136-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTDHDERTFV MVKPDGVQRG LIGDIVTRLE TKGLKMVGGK FMRIDEELAH
60 70 80 90 100
EHYAEHEDKP FFDGLVSFIT SGPVFAMVWE GADATRQVRQ LMGATDAQDA
110 120 130 140 150
APGTIRGDYG NDLGHNLIHG SDHEDEGANE REIALFFDDD ELVDWDRDAS
160
AWVYEDLADH D
Length:161
Mass (Da):18,065
Last modified:May 10, 2004 - v1
Checksum:i8A339F3F4D4C0AF3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB036344 Genomic DNA. Translation: BAB17308.1.
AE004437 Genomic DNA. Translation: AAG19540.1.
PIRiH84271.
RefSeqiWP_010902835.1. NC_002607.1.

Genome annotation databases

EnsemblBacteriaiAAG19540; AAG19540; VNG_1160G.
GeneIDi5954227.
KEGGihal:VNG1160G.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB036344 Genomic DNA. Translation: BAB17308.1.
AE004437 Genomic DNA. Translation: AAG19540.1.
PIRiH84271.
RefSeqiWP_010902835.1. NC_002607.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2AZ1X-ray2.35A/B/C/D/E/F1-161[»]
2AZ3X-ray2.20A/B/C/D/E/F/G/H/I1-161[»]
ProteinModelPortaliP61136.
SMRiP61136. Positions 4-158.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi64091.VNG1160G.

Proteomic databases

PaxDbiP61136.
PRIDEiP61136.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAG19540; AAG19540; VNG_1160G.
GeneIDi5954227.
KEGGihal:VNG1160G.

Phylogenomic databases

eggNOGiarCOG04313. Archaea.
COG0105. LUCA.
InParanoidiP61136.
KOiK00940.
OMAiVERFFME.
PhylomeDBiP61136.

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-15776.
BRENDAi2.7.4.6. 2552.

Miscellaneous databases

EvolutionaryTraceiP61136.

Family and domain databases

HAMAPiMF_00451. NDP_kinase.
InterProiIPR001564. Nucleoside_diP_kinase.
[Graphical view]
PfamiPF00334. NDK. 1 hit.
[Graphical view]
PRINTSiPR01243. NUCDPKINASE.
SMARTiSM00562. NDK. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "NDK from Halobacterium cutirubrum."
    Ishibashi M., Hiratsuka K., Yonezawa Y., Tokunaga H., Tokunaga M.
    Submitted (DEC-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700922 / JCM 11081 / NRC-1.
  3. "Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum."
    Besir H., Zeth K., Bracher A., Heider U., Ishibashi M., Tokunaga M., Oesterhelt D.
    FEBS Lett. 579:6595-6600(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH ATP ANALOG.

Entry informationi

Entry nameiNDK_HALSA
AccessioniPrimary (citable) accession number: P61136
Secondary accession number(s): P61137, Q9HQH5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 10, 2004
Last sequence update: May 10, 2004
Last modified: June 8, 2016
This is version 85 of the entry and version 1 of the sequence. [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

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.