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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei11 – 111ATPBy similarity
Binding sitei59 – 591ATPBy similarity
Binding sitei87 – 871ATPBy similarity
Binding sitei93 – 931ATPBy similarity
Binding sitei107 – 1071ATPBy similarity
Binding sitei117 – 1171ATPBy similarity
Active sitei120 – 1201Pros-phosphohistidine intermediateBy similarity

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

BioCyciAAEO224324:GJBH-1135-MONOMER.

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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 142142Nucleoside diphosphate kinasePRO_0000136936Add
BLAST

Keywords - PTMi

Phosphoprotein

Interactioni

Subunit structurei

Homotetramer.By similarity

Protein-protein interaction databases

STRINGi224324.aq_1590.

Structurei

Secondary structure

1
142
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 108Combined sources
Helixi12 – 176Combined sources
Helixi20 – 2910Combined sources
Beta strandi33 – 408Combined sources
Helixi44 – 507Combined sources
Helixi52 – 543Combined sources
Helixi60 – 678Combined sources
Beta strandi72 – 809Combined sources
Helixi82 – 909Combined sources
Helixi95 – 1017Combined sources
Helixi106 – 1105Combined sources
Beta strandi113 – 1164Combined sources
Beta strandi118 – 1214Combined sources
Helixi125 – 13511Combined sources
Helixi138 – 1403Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.Curated

Phylogenomic databases

eggNOGiENOG4108UGX. Bacteria.
COG0105. LUCA.
HOGENOMiHOG000224565.
InParanoidiO67528.
KOiK00940.
OMAiFPMVLEK.
OrthoDBiEOG67DPRV.

Family and domain databases

HAMAPiMF_00451. NDP_kinase.
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
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.
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.
OrthoDBiEOG67DPRV.

Enzyme and pathway databases

BioCyciAAEO224324:GJBH-1135-MONOMER.

Family and domain databases

HAMAPiMF_00451. NDP_kinase.
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...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: VF5.

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: February 17, 2016
This is version 99 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.