spacer
View the latest EBI news stories and important announcements...
more

spacer
Search The CSA
PDB ID
UNIPROT ID
EC Number

Catalytic Site Atlas

CSA LITERATURE entry for 1dek

E.C. name(deoxy)nucleoside-phosphate kinase
SpeciesBacteriophage t4 (Virus)
E.C. Number (IntEnz) 2.7.4.13
CSA Homologues of 1dek1del,
CSA Entries With UniProtID P04531
CSA Entries With EC Number 2.7.4.13
PDBe Entry 1dek
PDBSum Entry 1dek
MACiE Entry 1dek

Literature Report

IntroductionThe 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.
MechansimIn 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.
Reaction

Catalytic Sites for 1dek

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ArgA6868macie:sideChainContacts the gamma phosphate of ATP thus stabilising the pentavalent phosphate transition state that forms during the reaction.
HisA206206macie:sideChainContacts the gamma phosphate of ATP thus stabilises the pentavalent phosphate transition state that forms during the reaction.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ArgB6868macie:sideChainError

Literature References

Notes:
Teplyakov A
Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.
EMBO J 1996 15 3487-3497
PubMed: 8670851
spacer
spacer