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Protein

Nucleoside diphosphate kinase

Gene

ndk

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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 sitei9 – 91ATPUniRule annotation1 Publication
Binding sitei57 – 571ATPUniRule annotation1 Publication
Binding sitei85 – 851ATPUniRule annotation1 Publication
Binding sitei91 – 911ATPUniRule annotation1 Publication
Binding sitei102 – 1021ATPUniRule annotation1 Publication
Binding sitei112 – 1121ATPUniRule annotation1 Publication
Active sitei115 – 1151Pros-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

BioCyciTTHE300852:GH8R-197-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:TTHA0188
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
Proteomesi
  • UP000000532 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 – 137137Nucleoside diphosphate kinasePRO_0000137067Add
BLAST

Keywords - PTMi

Phosphoprotein

Interactioni

Subunit structurei

Homotetramer.UniRule annotation

Protein-protein interaction databases

STRINGi300852.TTHA0188.

Structurei

Secondary structure

1
137
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 86Combined sources
Helixi10 – 145Combined sources
Helixi18 – 2811Combined sources
Beta strandi31 – 388Combined sources
Helixi42 – 487Combined sources
Helixi50 – 523Combined sources
Beta strandi53 – 575Combined sources
Helixi58 – 658Combined sources
Beta strandi70 – 778Combined sources
Helixi80 – 889Combined sources
Turni93 – 953Combined sources
Helixi101 – 1055Combined sources
Beta strandi113 – 1164Combined sources
Helixi120 – 13011Combined sources
Helixi133 – 1353Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WKJX-ray2.00A/B1-137[»]
1WKKX-ray2.70A/B1-137[»]
1WKLX-ray2.20A/B1-137[»]
ProteinModelPortaliQ5SLV5.
SMRiQ5SLV5. Positions 1-137.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5SLV5.

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108UGX. Bacteria.
COG0105. LUCA.
HOGENOMiHOG000224564.
KOiK00940.
OMAiAEHSERP.
OrthoDBiEOG67DPRV.
PhylomeDBiQ5SLV5.

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.

Q5SLV5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MERTFVMIKP DGVRRGLVGE ILARFERKGF RIAALKLMQI SQELAERHYA
60 70 80 90 100
EHREKPFFPG LVRFITSGPV VAMVLEGPGV VAEVRKMMGA THPKDALPGT
110 120 130
IRGDFATTID ENVIHGSATL EDAQREIALF FRPEELL
Length:137
Mass (Da):15,344
Last modified:December 21, 2004 - v1
Checksum:i750E673CA9C9FE3E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008226 Genomic DNA. Translation: BAD70011.1.
RefSeqiWP_011227764.1. NC_006461.1.
YP_143454.1. NC_006461.1.

Genome annotation databases

EnsemblBacteriaiBAD70011; BAD70011; BAD70011.
GeneIDi3169489.
KEGGittj:TTHA0188.
PATRICi23955317. VBITheThe93045_0186.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008226 Genomic DNA. Translation: BAD70011.1.
RefSeqiWP_011227764.1. NC_006461.1.
YP_143454.1. NC_006461.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WKJX-ray2.00A/B1-137[»]
1WKKX-ray2.70A/B1-137[»]
1WKLX-ray2.20A/B1-137[»]
ProteinModelPortaliQ5SLV5.
SMRiQ5SLV5. Positions 1-137.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi300852.TTHA0188.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD70011; BAD70011; BAD70011.
GeneIDi3169489.
KEGGittj:TTHA0188.
PATRICi23955317. VBITheThe93045_0186.

Phylogenomic databases

eggNOGiENOG4108UGX. Bacteria.
COG0105. LUCA.
HOGENOMiHOG000224564.
KOiK00940.
OMAiAEHSERP.
OrthoDBiEOG67DPRV.
PhylomeDBiQ5SLV5.

Enzyme and pathway databases

BioCyciTTHE300852:GH8R-197-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ5SLV5.

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. "Complete genome sequence of Thermus thermophilus HB8."
    Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.
    Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HB8 / ATCC 27634 / DSM 579.
  2. "Crystallization and preliminary X-ray diffraction studies of nucleoside diphosphate kinase from Thermus thermophilus HB8."
    Takeishi S., Nakagawa N., Maoka N., Kihara M., Moriguchi M., Masui R., Kuramitsu S.
    Acta Crystallogr. D 59:1843-1845(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH ATP.

Entry informationi

Entry nameiNDK_THET8
AccessioniPrimary (citable) accession number: Q5SLV5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: December 21, 2004
Last modified: November 11, 2015
This is version 82 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.