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Protein

Nucleoside diphosphate kinase

Gene

ndk

Organism
Aquifex aeolicus (strain VF5)
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.

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei11ATPBy similarity1
Binding sitei59ATPBy similarity1
Binding sitei87ATPBy similarity1
Binding sitei93ATPBy similarity1
Binding sitei107ATPBy similarity1
Binding sitei117ATPBy similarity1
Active sitei120Pros-phosphohistidine intermediateBy similarity1

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

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:aq_1590
OrganismiAquifex aeolicus (strain VF5)
Taxonomic identifieri224324 [NCBI]
Taxonomic lineageiBacteriaAquificaeAquificalesAquificaceaeAquifex
Proteomesi
  • UP000000798 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001369361 – 142Nucleoside diphosphate kinaseAdd BLAST142

Keywords - PTMi

Phosphoprotein

Interactioni

Subunit structurei

Homotetramer.By similarity

Protein-protein interaction databases

STRINGi224324.aq_1590.

Structurei

Secondary structure

1142
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 10Combined sources8
Helixi12 – 17Combined sources6
Helixi20 – 29Combined sources10
Beta strandi33 – 40Combined sources8
Helixi44 – 50Combined sources7
Helixi52 – 54Combined sources3
Helixi60 – 67Combined sources8
Beta strandi72 – 80Combined sources9
Helixi82 – 90Combined sources9
Helixi95 – 101Combined sources7
Helixi106 – 110Combined sources5
Beta strandi113 – 116Combined sources4
Beta strandi118 – 121Combined sources4
Helixi125 – 135Combined sources11
Helixi138 – 140Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3ZTOX-ray1.47A1-142[»]
3ZTPX-ray1.37A/C1-142[»]
3ZTQX-ray2.10A/B/C/D/E/F/G/H1-142[»]
3ZTRX-ray2.30A/B/C/D/E/F/G/H/I/J/K/L1-142[»]
3ZTSX-ray2.30A/B/C/D/E/F/G/H/I/J/K/L1-142[»]
ProteinModelPortaliO67528.
SMRiO67528.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.Curated

Phylogenomic databases

eggNOGiENOG4108UGX. Bacteria.
COG0105. LUCA.
HOGENOMiHOG000224565.
InParanoidiO67528.
KOiK00940.
OMAiFPMVLEK.
OrthoDBiPOG091H040S.

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.

O67528-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVERTLIIV KPDAMEKGAL GKILDRFIQE GFQIKALKMF RFTPEKAGEF
60 70 80 90 100
YYVHRERPFF QELVEFMSSG PVVAAVLEGE DAIKRVREII GPTDSEEARK
110 120 130 140
VAPNSIRAQF GTDKGKNAIH ASDSPESAQY EICFIFSGLE IV
Length:142
Mass (Da):15,942
Last modified:August 1, 1998 - v1
Checksum:i189B5DFA0317E998
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC07481.1.
PIRiF70437.
RefSeqiNP_214093.1. NC_000918.1.
WP_010881031.1. NC_000918.1.

Genome annotation databases

EnsemblBacteriaiAAC07481; AAC07481; aq_1590.
GeneIDi1193151.
KEGGiaae:aq_1590.
PATRICi20960228. VBIAquAeo85532_1227.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC07481.1.
PIRiF70437.
RefSeqiNP_214093.1. NC_000918.1.
WP_010881031.1. NC_000918.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3ZTOX-ray1.47A1-142[»]
3ZTPX-ray1.37A/C1-142[»]
3ZTQX-ray2.10A/B/C/D/E/F/G/H1-142[»]
3ZTRX-ray2.30A/B/C/D/E/F/G/H/I/J/K/L1-142[»]
3ZTSX-ray2.30A/B/C/D/E/F/G/H/I/J/K/L1-142[»]
ProteinModelPortaliO67528.
SMRiO67528.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224324.aq_1590.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC07481; AAC07481; aq_1590.
GeneIDi1193151.
KEGGiaae:aq_1590.
PATRICi20960228. VBIAquAeo85532_1227.

Phylogenomic databases

eggNOGiENOG4108UGX. Bacteria.
COG0105. LUCA.
HOGENOMiHOG000224565.
InParanoidiO67528.
KOiK00940.
OMAiFPMVLEK.
OrthoDBiPOG091H040S.

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_AQUAE
AccessioniPrimary (citable) accession number: O67528
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: August 1, 1998
Last modified: November 2, 2016
This is version 102 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.