(deoxy)nucleoside-phosphate kinase

 

The deoxynucleotide kinase from phage T4 is able to catalyse the phosphorylation of GMP, methyl-CMP and TMP to the corresponding nucleotide diphosphate using ATP as the phosphate donor. This process is of particular interest because of the diverse specificity of the enzyme: most species deoxynucleotide kinases are only able to phosphorylate one dNMP, but owing to the selective pressure on the phage to have as small a genome as possible to allow easier infection of the bacteria, a wider specificity has developed. The sequence of the enzyme displays no homology to any other kinases, but does include the triphosphate binding consensus sequence.

 

Reference Protein and Structure

Sequence
P04531 UniProt (2.7.4.13) IPR027417 (Sequence Homologues) (PDB Homologues)
Biological species
Enterobacteria phage T4 (Virus) Uniprot
PDB
1dek - DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP (2.0 Å) PDBe PDBsum 1dek
Catalytic CATH Domains
1.10.238.70 CATHdb 3.40.50.300 CATHdb (see all for 1dek)
Cofactors
Magnesium(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:2.7.4.13)

2'-deoxynucleoside 5'-monophosphate(2-)
CHEBI:65317ChEBI
+
ATP(4-)
CHEBI:30616ChEBI
→
ADP(3-)
CHEBI:456216ChEBI
+
2'-deoxyribonucleoside 5'-diphosphate(3-)
CHEBI:73316ChEBI
Alternative enzyme names: Deoxynucleoside monophosphate kinase, Deoxynucleoside-5'-monophosphate kinase, Deoxyribonucleoside monophosphokinase, ATP:deoxynucleoside-phosphate phosphotransferase,

Enzyme Mechanism

Introduction

In line nucleophilic attack from the dNMP on the gamma phosphate of ATP seems the most likely mechanism for the reaction. This proceeds via a pentavalent phosphate transition state, stabilised by catalytic residues Arg68, His 206 and a catalytic Mg2+ ion whose location in the enzyme has not been confirmed.

Catalytic Residues Roles

UniProt PDB* (1dek)
Asp15 Asp15A Proposed to coordinate in a bidente manner to the Mg2+ ion important in catalysis in both activating the nucleophile and stabilising the transition state.
His206 His206A Contacts the gamma phosphate of ATP thus stabilises the pentavalent phosphate transition state that forms during the reaction. metal ligand, electrostatic stabiliser
Arg68 Arg68A Contacts the gamma phosphate of ATP thus stabilising the pentavalent phosphate transition state that forms during the reaction. electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

bimolecular nucleophilic substitution

References

  1. Teplyakov A et al. (1996), EMBO J, 15, 3487-3497. Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP. PMID:8670851.

Step 1.

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Catalytic Residues Roles

Residue Roles
Arg68A electrostatic stabiliser
His206A electrostatic stabiliser
His206A metal ligand

Chemical Components

ingold: bimolecular nucleophilic substitution

Step 1.

Contributors

Peter Sarkies, Gemma L. Holliday, Morwenna Hall