Nucleoside diphosphate kinase - Escherichia coli (strain K12)

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P0A763 (NDK_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 78. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Nucleoside diphosphate kinase
Short name=NDK
Short name=NDP kinase
EC=2.7.4.6

Alternative name(s):
Nucleoside-2-P kinase

Gene names

Name:	ndk
Ordered Locus Names:	b2518, JW2502

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	143 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. HAMAP-Rule MF_00451
Catalytic activity	ATP + nucleoside diphosphate = ADP + nucleoside triphosphate. HAMAP-Rule MF_00451
Cofactor	Magnesium By similarity. HAMAP-Rule MF_00451
Subunit structure	Homotetramer.
Subcellular location	Cytoplasm HAMAP-Rule MF_00451.
Sequence similarities	Belongs to the NDK family.

Ontologies

Keywords
Biological process	Nucleotide metabolism
Cellular component	Cytoplasm
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Kinase Transferase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	CTP biosynthetic process Inferred from electronic annotation. Source: HAMAP GTP biosynthetic process Inferred from electronic annotation. Source: HAMAP UTP biosynthetic process Inferred from electronic annotation. Source: HAMAP
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleoside diphosphate kinase activity Inferred from direct assay PubMed 214126. Source: EcoCyc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ung	P12295	3	EBI-370139,EBI-559403
ygfA	P0AC28	3	EBI-370139,EBI-555094

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.5 Ref.7 Ref.8

Chain

2 – 143

142

Nucleoside diphosphate kinase HAMAP-Rule MF_00451

PRO_0000136978

Sites

Active site

117

Pros-phosphohistidine intermediate

Binding site

ATP By similarity

Binding site

ATP By similarity

Binding site

ATP By similarity

Binding site

ATP By similarity

Binding site

104

ATP By similarity

Binding site

114

ATP By similarity

Amino acid modifications

Modified residue

119

Phosphoserine HAMAP-Rule MF_00451

Modified residue

121

Phosphoserine HAMAP-Rule MF_00451

Secondary structure

143

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P0A763 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 8C069C10043532EC
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FASTA

143

15,463

        10         20         30         40         50         60 
MAIERTFSII KPNAVAKNVI GNIFARFEAA GFKIVGTKML HLTVEQARGF YAEHDGKPFF 

        70         80         90        100        110        120 
DGLVEFMTSG PIVVSVLEGE NAVQRHRDLL GATNPANALA GTLRADYADS LTENGTHGSD 

       130        140 
SVESAAREIA YFFGEGEVCP RTR

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleoside diphosphate kinase from Escherichia coli; its overproduction and sequence comparison with eukaryotic enzymes." Hama H., Almaula N., Lerner C.G., Inouye S., Inouye M. Gene 105:31-36(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. Horiuchi T. DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Nucleoside diphosphokinase: a functional link between intermediary metabolism and nucleic acid synthesis." Ray N.B., Mathews C.K. Curr. Top. Cell. Regul. 33:343-357(1992) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-46.
[6]	"Nucleoside diphosphate kinase from Escherichia coli." Almaula N., Lu Q., Delgado J., Belkin S., Inouye M. J. Bacteriol. 177:2524-2529(1995) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION, PARTIAL PROTEIN SEQUENCE.
[7]	Frutiger S., Hughes G.J., Pasquali C., Hochstrasser D.F. Submitted (FEB-1996) to UniProtKB Cited for: PROTEIN SEQUENCE OF 2-12. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[8]	"Identification of phosphoproteins in Escherichia coli." Freestone P., Grant S., Toth I., Norris V. Mol. Microbiol. 15:573-580(1995) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-11, PHOSPHORYLATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X57555 Genomic DNA. Translation: CAA40780.1.
U00096 Genomic DNA. Translation: AAC75571.1.
AP009048 Genomic DNA. Translation: BAA16405.1.

PIR

JH0495.

RefSeq

NP_417013.1. NC_000913.2.
YP_490746.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2HUR	X-ray	1.62	A/B/C/D/E/F	2-142	[»]

ProteinModelPortal

P0A763.

SMR

P0A763. Positions 2-143.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-31870N.

IntAct

P0A763. 6 interactions.

MINT

MINT-1255778.

STRING

511145.b2518.

PTM databases

PhosSite

P0809416.

2D gel databases

SWISS-2DPAGE

P0A763.

Proteomic databases

PaxDb

P0A763.

PRIDE

P0A763.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75571; AAC75571; b2518.
BAA16405; BAA16405; BAA16405.

GeneID

12930715.
945611.

KEGG

ecj:Y75_p2471.
eco:b2518.

PATRIC

32120429. VBIEscCol129921_2617.

Organism-specific databases

EchoBASE

EB0644.

EcoGene

EG10650. ndk.

Phylogenomic databases

eggNOG

COG0105.

HOGENOM

HOG000224565.

K00940.

OMA

FRVVAMK.

ProtClustDB

PRK00668.

Enzyme and pathway databases

BioCyc

EcoCyc:NUCLEOSIDE-DIP-KIN-MONOMER.
ECOL316407:JW2502-MONOMER.
MetaCyc:NUCLEOSIDE-DIP-KIN-MONOMER.

Gene expression databases

Genevestigator

P0A763.

Family and domain databases

Gene3D

3.30.70.141. 1 hit.

HAMAP

MF_00451. NDP_kinase.

InterPro

IPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]

PANTHER

PTHR11349. PTHR11349. 1 hit.

Pfam

PF00334. NDK. 1 hit.
[Graphical view]

PRINTS

PR01243. NUCDPKINASE.

SMART

SM00562. NDK. 1 hit.
[Graphical view]

SUPFAM

SSF54919. NDK. 1 hit.

PROSITE

PS00469. NDP_KINASES. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P0A763.

Entry information

Entry name

NDK_ECOLI

Accession

Primary (citable) accession number: P0A763
Secondary accession number(s): P24233

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 7, 2005
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 78 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Sites

Amino acid modifications

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

2D gel databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents