Get   for     ? 
 Site search     ? 
Catalytic Site Atlas Version 2.2.12
Find Annotated Site: PDB code:
Swiss-Prot code:
EC number:
Help
CSA entry for 1dek
Original Entry
Title:
Phosphotransferase
Compound:
Deoxynucleoside monophosphate kinase
Mutant:
No
UniProt/Swiss-Prot:
P04531-KDNM_BPT4
EC Class:
2.7.4.13
Other CSA Entries:
Overview of all sites for 1dek
Homologues of 1dek
Entries for UniProt/Swiss-Prot: P04531
Entries for EC: 2.7.4.13
Other Databases:
PDB entry: 1dek
PDBsum entry: 1dek
UniProt/Swiss-Prot: P04531
IntEnz entry: 2.7.4.13
Literature Report:
Introduction:
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.
Mechanism:
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.
Sites:

Click to Display Catalytic Site (Get help with this section)
Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ARGA 68 68Sidechain
ElectrostaticTransition state
Contacts the gamma phosphate of ATP thus stabilising the pentavalent phosphate transition state that forms during the reaction.
Evidence from paper Evidence concerns Evidence type
PubMed ID 8670851 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 8670851 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
HISA 206 206Sidechain
ElectrostaticTransition state
Contacts the gamma phosphate of ATP thus stabilises the pentavalent phosphate transition state that forms during the reaction.
Evidence from paper Evidence concerns Evidence type
PubMed ID 8670851 Current protein Mutagenesis of residue
PubMed ID 8670851 Current protein Residue is positioned appropriately (ligand position known)
References:
1
Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.
A. Teplyakov and P. Sebastiao and G. Obmolova and A. Perrakis and G. S. Brush and M. J. Bessman and K. S. Wilson
EMBO J 15, (14) 3487-97, (1996).
8670851
Which EBI biological databases are available and how do I access them? EBI Site Map