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Overview for MACiE Entry M0150

Version history

General Information

EC Number: 2.7.4.6 (A member of the Transferases, Transferring phosphorus-containing groups, Phosphotransferases with a phosphate group as acceptor)

Enzyme Name: nucleoside-diphosphate kinase

Biological Species: Dictyostelium discoideum (Slime mould)

Catalytic Chain UniprotKB Accession Codes:

  • P22887 - Nucleoside diphosphate kinase, cytosolic

Representative PDB Code: 1ndp - ADENOSINE 5'-DIPHOSPHATE BINDING AND THE ACTIVE SITE OF NUCLEOSIDEDIPHOSPHATE KINASE (Resolution = 2.20 Å).

Catalytic CATH Codes:

"Other" CATH Codes:

Display structure information

Overall Reaction:

Image of ATP

Image of nucleoside diphosphate

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Image of nucleoside triphosphate

Image of ADP

ATP
C00002
CHEBI:30616
nucleoside diphosphate
C11479
CHEBI:57930
nucleoside triphosphate
C00201
CHEBI:61557
ADP
C00008
CHEBI:456216

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Stepwise Description of the Reaction

Step 1The gamma phosphate of ATP deprotonates His122. His122 then attacks the gamma phosphate of ATP in a nucleophilic substitution, releasing the ADP product.
Step 2The nucleoside diphosphate substrate attacks the phosphate of the phosphorylated His122 in a nucleophilic substitution. The released His122 then deprotonates the triphosphate giving the nucleoside triphosphate product.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
His 122 B Side Chain
Lys 16 B Side Chain
Tyr 56 B Side Chain
Asn 119 B Side Chain
Glu 133 B Side Chain

Metal Cofactors for M0150

Type Het group Number Chain
magnesium MG 156 A Overview

References

  1. M. C. Hutter et al. (2002), Chembiochem, 3, 643-651. The mechanism of phosphorylation of natural nucleosides and anti-HIV analogues by nucleoside diphosphate kinase is independent of their sugar substituents.
    Medline: 12324998
  2. B. Schneider et al. (2001), Eur. J. Biochem., 268, 1964-1971. Mechanism of phosphoryl transfer by nucleoside diphosphate kinase pH dependence and role of the active site Lys16 and Tyr56 residues.
    Medline: 11277918
  3. S. Gallois-Montbrun et al. (2003), Mol. Pharmacol., 63, 538-546. Structural analysis of the activation of ribavirin analogs by NDP kinase: comparison with other ribavirin targets.
    Medline: 12606760
  4. Gonin P et al. (1999), Biochemistry, 38, 7265-7272. Catalytic mechanism of nucleoside diphosphate kinase investigated using nucleotide analogues, viscosity effects, and X-ray crystallography.
    Medline: 10353838
  5. Admiraal SJ et al. (1999), Biochemistry, 38, 4701-4711. Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase.
    Medline: 10200157

Homologue information for M0150 (1ndp)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ

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nucleoside diphosphate kinase activity (molecular function)
ATP binding (molecular function)
nucleoside diphosphate phosphorylation (biological process)
GTP biosynthetic process (biological process)
UTP biosynthetic process (biological process)
CTP biosynthetic process (biological process)
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