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Protein

Nucleoside diphosphate kinase

Gene

ndk

Organism
Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827)
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 (By similarity).By similarity

Catalytic activityi

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.PROSITE-ProRule annotation

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei11ATPBy similarity1
Binding sitei120ATPBy similarity1
Binding sitei126ATPBy similarity1
Binding sitei137ATPBy similarity1
Binding sitei157ATPBy similarity1
Active sitei160Pros-phosphohistidine intermediatePROSITE-ProRule 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

BRENDAi2.7.4.6. 5239.

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:PAE1561
OrganismiPyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827)
Taxonomic identifieri178306 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiThermoprotealesThermoproteaceaePyrobaculum
Proteomesi
  • UP000002439 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001370971 – 183Nucleoside diphosphate kinaseAdd BLAST183

Keywords - PTMi

Phosphoprotein

Interactioni

Protein-protein interaction databases

STRINGi178306.PAE1561.

Structurei

Secondary structure

1183
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 10Combined sources6
Helixi12 – 16Combined sources5
Helixi20 – 30Combined sources11
Beta strandi33 – 40Combined sources8
Helixi44 – 50Combined sources7
Helixi55 – 72Combined sources18
Helixi76 – 80Combined sources5
Helixi85 – 100Combined sources16
Beta strandi105 – 112Combined sources8
Helixi115 – 123Combined sources9
Helixi128 – 130Combined sources3
Helixi136 – 140Combined sources5
Helixi145 – 150Combined sources6
Beta strandi158 – 161Combined sources4
Helixi165 – 175Combined sources11
Helixi178 – 180Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1XQIX-ray2.50A/B/C1-183[»]
ProteinModelPortaliQ8ZWY4.
SMRiQ8ZWY4.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8ZWY4.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni56 – 88InsertAdd BLAST33

Sequence similaritiesi

Belongs to the NDK family.Curated

Phylogenomic databases

eggNOGiarCOG04313. Archaea.
COG0105. LUCA.
HOGENOMiHOG000224564.
InParanoidiQ8ZWY4.
KOiK00940.
OMAiKIVAMKM.
OrthoDBiPOG093Z0ECU.

Family and domain databases

Gene3Di3.30.70.141. 1 hit.
InterProiView protein in InterPro
IPR034907. NDK-like_dom.
IPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
PfamiView protein in Pfam
PF00334. NDK. 2 hits.
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.

Q8ZWY4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPVEKTLLIL KPDAVARGLV GEIISRFEKA GLKIVALKMV KASPEEIERF
60 70 80 90 100
YPSSEEWLRS AGQKLLKAYQ ELGIDPRAKI GTDDPVEVGR IIKRSLVKYM
110 120 130 140 150
TSGPIVVMVL KGNRAVEIVR KLVGPTSPHS APPGTIRGDY SIDSPDLAAE
160 170 180
EGRVVFNLVH ASDSPSEAER EIRFWFREEE VLE
Length:183
Mass (Da):20,322
Last modified:March 5, 2002 - v1
Checksum:iCFEC6F1DD9EC93FC
GO

Sequence cautioni

The sequence AAL63565 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009441 Genomic DNA. Translation: AAL63565.1. Different initiation.

Genome annotation databases

EnsemblBacteriaiAAL63565; AAL63565; PAE1561.
KEGGipai:PAE1561.
PATRICifig|178306.9.peg.1155.

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.

Entry informationi

Entry nameiNDK_PYRAE
AccessioniPrimary (citable) accession number: Q8ZWY4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 5, 2002
Last sequence update: March 5, 2002
Last modified: July 5, 2017
This is version 103 of the entry and version 1 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