ECMDB

Identification

Name:

Nucleoside diphosphate kinase

Synonyms:

NDK
NDP kinase
Nucleoside-2-P kinase

Gene Name:

ndk

Enzyme Class:

2.7.4.6

Biological Properties

General Function:

Involved in nucleoside diphosphate kinase activity

Specific 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

Cellular Location:

Cytoplasm

SMPDB Pathways:

Pyrimidine metabolism PW000942
purine nucleotides de novo biosynthesis PW000910
purine nucleotides de novo biosynthesis 1435709748 PW000960
purine nucleotides de novo biosynthesis 2 PW002033

KEGG Pathways:

Metabolic pathways eco01100
Purine metabolism ec00230
Pyrimidine metabolism ec00240

Transports:

Transport References:

Not Available

KEGG Reactions:

1.0

↔

1.0

1.0Adenosine triphosphate + 1.0Uridine 5'-diphosphate ↔ 1.0ADP + 1.0Uridine triphosphate
ReactionCard

1.0

↔

1.0

1.0Adenosine triphosphate + 1.0dGDP ↔ 1.0ADP + 1.0dGTP
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1.0

↔

1.0

1.0Adenosine triphosphate + 1.0Guanosine diphosphate ↔ 1.0ADP + 1.0Guanosine triphosphate
ReactionCard

1.0

↔

1.0

1.0Adenosine triphosphate + 1.0dCDP ↔ 1.0ADP + 1.0dCTP
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1.0

↔

1.0

1.0Adenosine triphosphate + 1.0dTDP ↔ 1.0ADP + 1.0Thymidine 5'-triphosphate
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1.0

↔

1.0

1.0Adenosine triphosphate + 1.0dADP ↔ 1.0ADP + 1.0dATP
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1.0

↔

1.0

1.0Adenosine triphosphate + 1.0dUDP ↔ 1.0ADP + 1.0Deoxyuridine triphosphate
ReactionCard

1.0

↔

1.0

1.0Adenosine triphosphate + 1.0CDP ↔ 1.0ADP + 1.0Cytidine triphosphate
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1.0

↔

1.0

1.0Adenosine triphosphate + 1.0IDP ↔ 1.0ADP + 1.0Inosine triphosphate
ReactionCard

1.0

1.0dGDP

↔

1.0

1.0Adenosine triphosphate + 1.0dGDP ↔ 1.0ADP + 1.0dGTP
ReactionCard

1.0

1.0dUDP

↔

1.0

1.0Adenosine triphosphate + 1.0dUDP ↔ 1.0ADP + 1.0Deoxyuridine triphosphate
ReactionCard

1.0

↔

1.0

1.0Adenosine triphosphate + 1.0DIDP ↔ 1.0ADP + 1.02'-Deoxyinosine triphosphate
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1.0

1.0NDP

↔

1.0

1.0Nucleoside triphosphate

1.0Adenosine triphosphate + 1.0NDP ↔ 1.0ADP + 1.0Nucleoside triphosphate
ReactionCard

SMPDB Reactions:

1.0

→

1.0Adenosine diphosphate

1.0

1.0Guanosine diphosphate + 1.0Adenosine triphosphate → 1.0Adenosine diphosphate + 1.0Guanosine triphosphate + 1.0ADP
ReactionCard

1.0dGDP

1.0

→

1.0Adenosine diphosphate

1.0

1.0dGDP + 1.0Adenosine triphosphate + 1.0dGDP → 1.0Adenosine diphosphate + 1.0dGTP + 1.0ADP
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1.0dADP

1.0

→

1.0Adenosine diphosphate

1.0dATP

1.0

1.0dADP + 1.0Adenosine triphosphate + 1.0dADP → 1.0Adenosine diphosphate + 1.0dATP + 1.0ADP + 1.0dATP
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1.0Uridine 5'-diphosphate

1.0

→

1.0Uridine triphosphate

1.0Adenosine diphosphate

1.0

1.0Uridine 5'-diphosphate + 1.0Adenosine triphosphate + 1.0Uridine 5'-diphosphate → 1.0Uridine triphosphate + 1.0Adenosine diphosphate + 1.0Uridine triphosphate + 1.0ADP
ReactionCard

1.0

→

1.0Adenosine diphosphate

1.0

1.0dCDP + 1.0Adenosine triphosphate → 1.0Adenosine diphosphate + 1.0dCTP + 1.0ADP
ReactionCard

1.0dUDP

1.0

→

1.0Adenosine diphosphate

1.0

1.0dUDP + 1.0Adenosine triphosphate + 1.0dUDP → 1.0Adenosine diphosphate + 1.0Deoxyuridine triphosphate + 1.0ADP
ReactionCard

1.0

→

1.0Adenosine diphosphate

1.0

1.0Adenosine triphosphate + 1.0dTDP → 1.0Adenosine diphosphate + 1.0Thymidine 5'-triphosphate + 1.0ADP
ReactionCard

EcoCyc Reactions:

1.0

↔

1.0

1.0Adenosine triphosphate + 1.0Uridine 5'-diphosphate ↔ 1.0ADP + 1.0Uridine triphosphate
ReactionCard

1.0

↔

1.0

1.0Adenosine triphosphate + 1.0dGDP ↔ 1.0ADP + 1.0dGTP
ReactionCard

1.0

↔

1.0

1.0Adenosine triphosphate + 1.0Guanosine diphosphate ↔ 1.0ADP + 1.0Guanosine triphosphate
ReactionCard

1.0

↔

1.0

1.0Adenosine triphosphate + 1.0dCDP ↔ 1.0ADP + 1.0dCTP
ReactionCard

1.0

↔

1.0

1.0Adenosine triphosphate + 1.0dTDP ↔ 1.0ADP + 1.0Thymidine 5'-triphosphate
ReactionCard

1.0

↔

1.0

1.0Adenosine triphosphate + 1.0dADP ↔ 1.0ADP + 1.0dATP
ReactionCard

1.0

↔

1.0

1.0Adenosine triphosphate + 1.0dUDP ↔ 1.0ADP + 1.0Deoxyuridine triphosphate
ReactionCard

1.0

↔

1.0

1.0Adenosine triphosphate + 1.0CDP ↔ 1.0ADP + 1.0Cytidine triphosphate
ReactionCard

Complex Reactions:

1.0

1.0nucleoside diphosphate

→

1.0

1.0nucleoside triphosphate

1.0Adenosine triphosphate + 1.0nucleoside diphosphate → 1.0ADP + 1.0nucleoside triphosphate
ReactionCard

Metabolites:

ECMDB ID	Name	View
ECMDB04063	2'-Deoxyinosine triphosphate	MetaboCard
ECMDB00538	Adenosine triphosphate	MetaboCard
ECMDB01341	ADP	MetaboCard
ECMDB01546	CDP	MetaboCard
ECMDB00082	Cytidine triphosphate	MetaboCard
ECMDB21326	dADP	MetaboCard
ECMDB01532	dATP	MetaboCard
ECMDB01245	dCDP	MetaboCard
ECMDB00998	dCTP	MetaboCard
ECMDB01191	Deoxyuridine triphosphate	MetaboCard
ECMDB00960	dGDP	MetaboCard
ECMDB01440	dGTP	MetaboCard
ECMDB03536	DIDP	MetaboCard
ECMDB01274	dTDP	MetaboCard
ECMDB01000	dUDP	MetaboCard
ECMDB01201	Guanosine diphosphate	MetaboCard
ECMDB01273	Guanosine triphosphate	MetaboCard
ECMDB03335	IDP	MetaboCard
ECMDB00189	Inosine triphosphate	MetaboCard
ECMDB01342	Thymidine 5'-triphosphate	MetaboCard
ECMDB00295	Uridine 5'-diphosphate	MetaboCard
ECMDB00285	Uridine triphosphate	MetaboCard

GO Classification:

Function
adenyl nucleotide binding
adenyl ribonucleotide binding
ATP binding
binding
catalytic activity
nucleoside binding
nucleoside diphosphate kinase activity
phosphotransferase activity, phosphate group as acceptor
purine nucleoside binding
transferase activity
transferase activity, transferring phosphorus-containing groups
Process
cellular nitrogen compound metabolic process
CTP biosynthetic process
GTP biosynthetic process
metabolic process
nitrogen compound metabolic process
nucleobase, nucleoside and nucleotide metabolic process
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
nucleoside phosphate metabolic process
nucleotide metabolic process
purine nucleoside triphosphate biosynthetic process
purine nucleotide biosynthetic process
purine nucleotide metabolic process
purine ribonucleoside triphosphate biosynthetic process
pyrimidine nucleoside triphosphate biosynthetic process
pyrimidine nucleotide biosynthetic process
pyrimidine nucleotide metabolic process
pyrimidine ribonucleoside triphosphate biosynthetic process
UTP biosynthetic process

Gene Properties

Blattner:

b2518

Gene Orientation

Counterclockwise

Centisome Percentage:

56.95

Left Sequence End

2642455

Right Sequence End

2642886

Gene Sequence:

>432 bp
ATGACAATCCATAAGAAAGGTCAGGCACACTGGGAAGGCGATATCAAACGCGGGAAGGGA
ACAGTATCCACCGAGAGTGGCGTGCTGAACCAACAGCCGTATGGATTTAACACGCGTTTT
GAAGGCGAAAAAGGAACCAACCCTGAAGAACTGATTGGCGCAGCGCATGCCGCATGTTTC
TCAATGGCGCTTTCATTAATGCTGGGGGAAGCGGGATTCACGCCAACATCGATTGATACC
ACCGCCGATGTGTCGCTGGATAAAGTGGATGCCGGTTTTGCGATTACGAAAATCGCACTG
AAGAGTGAAGTTGCGGTGCCGGGTATTGATGCCTCTACCTTTGACGGCATAATCCAGAAA
GCAAAAGCAGGATGCCCGGTCTCTCAGGTACTGAAAGCGGAAATTACGCTGGATTACCAG
TTGAAATCGTAA

Protein Properties

Pfam Domain Function:

NDK (PF00334 )

Protein Residues:

143

Protein Molecular Weight:

15463

Protein Theoretical pI:

Signaling Regions:

None

Transmembrane Regions:

None

Protein Sequence:

>Nucleoside diphosphate kinase
MAIERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFF
DGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSD
SVESAAREIAYFFGEGEVCPRTR

References

External Links:

Resource	Link
Uniprot ID:	P0A763
Uniprot Name:	NDK_ECOLI
GenBank Gene ID:	AP009048
Genebank Protein ID:	1742412
Ecogene ID:	EG10650
Ecocyc:	EG10650
ColiBase:	b2518
Kegg Gene:	b2518
EchoBASE ID:	EB0644
CCDB:	NDK_ECOLI
BacMap:	16130443

General Reference:

Almaula, N., Lu, Q., Delgado, J., Belkin, S., Inouye, M. (1995). "Nucleoside diphosphate kinase from Escherichia coli." J Bacteriol 177:2524-2529. Pubmed: 7730286
Blattner, F. R., Plunkett, G. 3rd, 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. (1997). "The complete genome sequence of Escherichia coli K-12." Science 277:1453-1462. Pubmed: 9278503
Freestone, P., Grant, S., Toth, I., Norris, V. (1995). "Identification of phosphoproteins in Escherichia coli." Mol Microbiol 15:573-580. Pubmed: 7783627
Hama, H., Almaula, N., Lerner, C. G., Inouye, S., Inouye, M. (1991). "Nucleoside diphosphate kinase from Escherichia coli; its overproduction and sequence comparison with eukaryotic enzymes." Gene 105:31-36. Pubmed: 1657712
Hayashi, K., Morooka, N., Yamamoto, Y., Fujita, K., Isono, K., Choi, S., Ohtsubo, E., Baba, T., Wanner, B. L., Mori, H., Horiuchi, T. (2006). "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Mol Syst Biol 2:2006.0007. Pubmed: 16738553
Ray, N. B., Mathews, C. K. (1992). "Nucleoside diphosphokinase: a functional link between intermediary metabolism and nucleic acid synthesis." Curr Top Cell Regul 33:343-357. Pubmed: 1323446
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., Horiuchi, T., et, a. l. .. (1997). "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." DNA Res 4:91-113. Pubmed: 9205837

Nucleoside diphosphate kinase (P0A763)