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Protein

Nucleoside diphosphate kinase

Gene

ndk

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 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.

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei11ATPBy similarity1
Binding sitei59ATPBy similarity1
Binding sitei87ATPBy similarity1
Binding sitei93ATPBy similarity1
Binding sitei104ATPBy similarity1
Binding sitei114ATPBy similarity1
Active sitei117Pros-phosphohistidine intermediate1

GO - Molecular functioni

  • ATP binding Source: UniProtKB-HAMAP
  • metal ion binding Source: UniProtKB-KW
  • nucleoside diphosphate kinase activity Source: EcoCyc

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

BioCyciEcoCyc:NUCLEOSIDE-DIP-KIN-MONOMER.
ECOL316407:JW2502-MONOMER.
MetaCyc:NUCLEOSIDE-DIP-KIN-MONOMER.
BRENDAi2.7.4.6. 2026.

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:b2518, JW2502
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10650. ndk.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved3 Publications
ChainiPRO_00001369782 – 143Nucleoside diphosphate kinaseAdd BLAST142

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei119Phosphoserine1 Publication1
Modified residuei121Phosphoserine1 Publication1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiP0A763.
PaxDbiP0A763.
PRIDEiP0A763.

2D gel databases

SWISS-2DPAGEP0A763.

PTM databases

iPTMnetiP0A763.

Interactioni

Subunit structurei

Homotetramer.

Binary interactionsi

WithEntry#Exp.IntActNotes
ungP122953EBI-370139,EBI-559403
ygfAP0AC283EBI-370139,EBI-555094

Protein-protein interaction databases

BioGridi4259709. 16 interactors.
DIPiDIP-31870N.
IntActiP0A763. 7 interactors.
MINTiMINT-1255778.
STRINGi511145.b2518.

Structurei

Secondary structure

1143
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 10Combined sources8
Helixi12 – 16Combined sources5
Helixi20 – 29Combined sources10
Beta strandi33 – 40Combined sources8
Helixi44 – 50Combined sources7
Helixi52 – 54Combined sources3
Helixi60 – 67Combined sources8
Beta strandi72 – 80Combined sources9
Helixi82 – 90Combined sources9
Turni95 – 97Combined sources3
Helixi103 – 107Combined sources5
Beta strandi109 – 111Combined sources3
Beta strandi115 – 118Combined sources4
Helixi122 – 132Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2HURX-ray1.62A/B/C/D/E/F2-143[»]
ProteinModelPortaliP0A763.
SMRiP0A763.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A763.

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.Curated

Phylogenomic databases

eggNOGiENOG4108UGX. Bacteria.
COG0105. LUCA.
HOGENOMiHOG000224565.
InParanoidiP0A763.
KOiK00940.
OMAiAEHSERP.
PhylomeDBiP0A763.

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.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A763-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAIERTFSII KPNAVAKNVI GNIFARFEAA GFKIVGTKML HLTVEQARGF
60 70 80 90 100
YAEHDGKPFF DGLVEFMTSG PIVVSVLEGE NAVQRHRDLL GATNPANALA
110 120 130 140
GTLRADYADS LTENGTHGSD SVESAAREIA YFFGEGEVCP RTR
Length:143
Mass (Da):15,463
Last modified:January 23, 2007 - v2
Checksum:i8C069C10043532EC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X57555 Genomic DNA. Translation: CAA40780.1.
U00096 Genomic DNA. Translation: AAC75571.1.
AP009048 Genomic DNA. Translation: BAA16405.1.
PIRiJH0495.
RefSeqiNP_417013.1. NC_000913.3.
WP_000963837.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75571; AAC75571; b2518.
BAA16405; BAA16405; BAA16405.
GeneIDi945611.
KEGGiecj:JW2502.
eco:b2518.
PATRICi32120429. VBIEscCol129921_2617.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X57555 Genomic DNA. Translation: CAA40780.1.
U00096 Genomic DNA. Translation: AAC75571.1.
AP009048 Genomic DNA. Translation: BAA16405.1.
PIRiJH0495.
RefSeqiNP_417013.1. NC_000913.3.
WP_000963837.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2HURX-ray1.62A/B/C/D/E/F2-143[»]
ProteinModelPortaliP0A763.
SMRiP0A763.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259709. 16 interactors.
DIPiDIP-31870N.
IntActiP0A763. 7 interactors.
MINTiMINT-1255778.
STRINGi511145.b2518.

PTM databases

iPTMnetiP0A763.

2D gel databases

SWISS-2DPAGEP0A763.

Proteomic databases

EPDiP0A763.
PaxDbiP0A763.
PRIDEiP0A763.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75571; AAC75571; b2518.
BAA16405; BAA16405; BAA16405.
GeneIDi945611.
KEGGiecj:JW2502.
eco:b2518.
PATRICi32120429. VBIEscCol129921_2617.

Organism-specific databases

EchoBASEiEB0644.
EcoGeneiEG10650. ndk.

Phylogenomic databases

eggNOGiENOG4108UGX. Bacteria.
COG0105. LUCA.
HOGENOMiHOG000224565.
InParanoidiP0A763.
KOiK00940.
OMAiAEHSERP.
PhylomeDBiP0A763.

Enzyme and pathway databases

BioCyciEcoCyc:NUCLEOSIDE-DIP-KIN-MONOMER.
ECOL316407:JW2502-MONOMER.
MetaCyc:NUCLEOSIDE-DIP-KIN-MONOMER.
BRENDAi2.7.4.6. 2026.

Miscellaneous databases

EvolutionaryTraceiP0A763.
PROiP0A763.

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_ECOLI
AccessioniPrimary (citable) accession number: P0A763
Secondary accession number(s): P24233
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 105 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.