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

GO - Biological processi

Keywordsi

Molecular functionKinase, Transferase
Biological processNucleotide metabolism
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:NUCLEOSIDE-DIP-KIN-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

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

PaxDbiP0A763.
PRIDEiP0A763.

2D gel databases

SWISS-2DPAGEiP0A763.

PTM databases

iPTMnetiP0A763.

Interactioni

Subunit structurei

Homotetramer.

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi4259709. 16 interactors.
DIPiDIP-31870N.
IntActiP0A763. 7 interactors.
MINTiMINT-1255778.
STRINGi316385.ECDH10B_2684.

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.
PhylomeDBiP0A763.

Family and domain databases

Gene3Di3.30.70.141. 1 hit.
HAMAPiMF_00451. NDP_kinase. 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. 1 hit.
PRINTSiPR01243. NUCDPKINASE.
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.

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.
PATRICifig|1411691.4.peg.4218.

Similar proteinsi

Entry informationi

Entry nameiNDK_ECOLI
AccessioniPrimary (citable) accession number: P0A763
Secondary accession number(s): P24233
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: January 23, 2007
Last modified: August 30, 2017
This is version 110 of the entry and version 2 of the sequence. See 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