Reviewed, UniProtKB/Swiss-Prot P0A763 (NDK_ECOLI)

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) [Complete 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 MF_00451
Catalytic activity	ATP + nucleoside diphosphate = ADP + nucleoside triphosphate. HAMAP MF_00451
Cofactor	Magnesium By similarity.
Subunit structure	Homotetramer. HAMAP MF_00451
Subcellular location	Cytoplasm. HAMAP 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
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 magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleoside diphosphate kinase activity Inferred from electronic annotation. Source: HAMAP protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ygfA	P0AC28	1	EBI-370139,EBI-555094

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.5 Ref.7 Ref.8

Chain

2 – 143

142

Nucleoside diphosphate kinase HAMAP MF_00451

PRO_0000136978

Sites

Active site

117

1

Pros-phosphohistidine intermediate HAMAP MF_00451

Binding site

11

1

ATP By similarity

Binding site

59

1

ATP By similarity

Binding site

87

1

ATP By similarity

Binding site

93

1

ATP By similarity

Binding site

104

1

ATP By similarity

Binding site

114

1

ATP By similarity

Amino acid modifications

Modified residue

119

1

Phosphoserine HAMAP MF_00451

Modified residue

121

1

Phosphoserine HAMAP MF_00451

Secondary structure

1

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143

Helix Strand Turn

Details...

Beta strand

3 – 10

8

Helix

12 – 16

5

Helix

20 – 29

10

Beta strand

33 – 40

8

Helix

44 – 50

7

Helix

52 – 54

3

Helix

60 – 67

8

Beta strand

72 – 80

9

Helix

82 – 90

9

Turn

95 – 97

3

Helix

103 – 107

5

Beta strand

109 – 111

3

Beta strand

115 – 118

4

Helix

122 – 132

11

Sequences

	Sequence		Length	Mass (Da)
	P0A763-1 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 8C069C10043532EC	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

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: 1657712] [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. , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T. DNA Res. 4:91-113(1997) [PubMed: 9205837] [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: 9278503] [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: 16738553] [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: 1323446] [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: 7730286] [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: 7783627] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-11, PHOSPHORYLATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

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

PIR

JH0495.

RefSeq

AP_003104.1.
NP_417013.1.

3D structure databases

PDBPDBe

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

ModBase

Search...

Protein-protein interaction databases

IntAct

P0A763. 5 interactions.

STRING

P0A763.

PTM databases

PhosSite

P0A763.

2-D gel databases

SWISS-2DPAGE

P0A763.

Proteomic databases

PRIDE

P0A763.

Genome annotation databases

GeneID

945611.

GenomeReviews

Gene locus JW2502 in contig AP009048_GR.
Gene locus b2518 in contig U00096_GR.

KEGG

ecj:JW2502.
eco:b2518.

Organism-specific databases

EchoBASE

EB0644.

EcoGene

EG10650. ndk.

CMR

Search...

Phylogenomic databases

HOGENOM

P0A763.

OMA

NLTGAIT.

Enzyme and pathway databases

BioCyc

EcoCyc:NUCLEOSIDE-DIP-KIN-MON.
MetaCyc:NUCLEOSIDE-DIP-KIN-MON.

Gene expression databases

Genevestigator

P0A763.

Family and domain databases

HAMAP

MF_00451.
[Tree]

InterPro

IPR001564. Nuc_diP_kinase_core.
[Graphical view]

PANTHER

PTHR11349. Nuc_diP_kinase_core. 1 hit.

Pfam

PF00334. NDK. 1 hit.
[Graphical view]

PRINTS

PR01243. NUCDPKINASE.

ProDom

PD001018. NDK. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00562. NDK. 1 hit.
[Graphical view]

PROSITE

PS00469. NDP_KINASES. 1 hit.
[Graphical view]

ProtoNet

Search...

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:	November 3, 2009
This is version 46 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)