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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei11 – 111ATPBy similarity
Binding sitei120 – 1201ATPBy similarity
Binding sitei126 – 1261ATPBy similarity
Binding sitei137 – 1371ATPBy similarity
Binding sitei157 – 1571ATPBy similarity
Active sitei160 – 1601Pros-phosphohistidine intermediatePROSITE-ProRule 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

BioCyciPAER178306:GCEO-1106-MONOMER.
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

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 183183Nucleoside diphosphate kinasePRO_0000137097Add
BLAST

Keywords - PTMi

Phosphoprotein

Interactioni

Protein-protein interaction databases

STRINGi178306.PAE1561.

Structurei

Secondary structure

1
183
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 106Combined sources
Helixi12 – 165Combined sources
Helixi20 – 3011Combined sources
Beta strandi33 – 408Combined sources
Helixi44 – 507Combined sources
Helixi55 – 7218Combined sources
Helixi76 – 805Combined sources
Helixi85 – 10016Combined sources
Beta strandi105 – 1128Combined sources
Helixi115 – 1239Combined sources
Helixi128 – 1303Combined sources
Helixi136 – 1405Combined sources
Helixi145 – 1506Combined sources
Beta strandi158 – 1614Combined sources
Helixi165 – 17511Combined sources
Helixi178 – 1803Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1XQIX-ray2.50A/B/C1-183[»]
ProteinModelPortaliQ8ZWY4.
SMRiQ8ZWY4. Positions 2-183.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8ZWY4.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni56 – 8833InsertAdd
BLAST

Sequence similaritiesi

Belongs to the NDK family.Curated

Phylogenomic databases

eggNOGiarCOG04313. Archaea.
COG0105. LUCA.
HOGENOMiHOG000224564.
InParanoidiQ8ZWY4.
KOiK00940.
OMAiAEHSERP.

Family and domain databases

InterProiIPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]
PfamiPF00334. NDK. 2 hits.
[Graphical view]
SMARTiSM00562. NDK. 1 hit.
[Graphical view]
PROSITEiPS00469. NDP_KINASES. 1 hit.
[Graphical view]

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.

Cross-referencesi

Sequence databases

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1XQIX-ray2.50A/B/C1-183[»]
ProteinModelPortaliQ8ZWY4.
SMRiQ8ZWY4. Positions 2-183.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi178306.PAE1561.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL63565; AAL63565; PAE1561.
KEGGipai:PAE1561.

Phylogenomic databases

eggNOGiarCOG04313. Archaea.
COG0105. LUCA.
HOGENOMiHOG000224564.
InParanoidiQ8ZWY4.
KOiK00940.
OMAiAEHSERP.

Enzyme and pathway databases

BioCyciPAER178306:GCEO-1106-MONOMER.
BRENDAi2.7.4.6. 5239.

Miscellaneous databases

EvolutionaryTraceiQ8ZWY4.

Family and domain databases

InterProiIPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]
PfamiPF00334. NDK. 2 hits.
[Graphical view]
SMARTiSM00562. NDK. 1 hit.
[Graphical view]
PROSITEiPS00469. NDP_KINASES. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNDK_PYRAE
AccessioniPrimary (citable) accession number: Q8ZWY4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 5, 2002
Last sequence update: March 5, 2002
Last modified: June 8, 2016
This is version 97 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.