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Catalytic Site Atlas

CSA LITERATURE entry for 1ltq

E.C. namepolynucleotide 5'-hydroxyl-kinase
SpeciesBacteriophage t4 (Virus)
E.C. Number (IntEnz) 2.7.1.78
CSA Homologues of 1ltqThere are 32 Homologs
CSA Entries With UniProtID P06855
CSA Entries With EC Number 2.7.1.78
PDBe Entry 1ltq
PDBSum Entry 1ltq
MACiE Entry 1ltq

Literature Report

IntroductionThis enzyme catalyses 5'-hydroxyl kinase, 3'-phosphatase and 2',3'-cyclic phosphodiesterase activities. These activities modify the ends of nicked tRNA generated by bacterial response to infection. These catalytic activities are dependent on magnesium as a cofactor. The kinase activity resides in an N-terminal domain, whilst the phosphatase activity resides in the C-terminal domain.
T4 PNK also has the ability to overcome some bacterial suicide defence mechanisms.
It is a member of a family of 5'-kinase/3'-phosphatases that mend broken strands in nucleic acids in conjunction with a RNA/DNA ligase. The kinase domain belongs to the adenylate kinase family whilst the phosphatase domain belongs to the L-2-haloacid dehalogenase.
MechansimPNK catalyses the transfer of the gamma-phosphate from adenosine triphosphate or other nucleoside triphosphates to the 5'-OH of polynucleotides. The activity proceeds via an ordered sequential mechanism. Phosphoryl transfer results in an inversion of configuration at the phosphorous.
The attacking nucleophile is the 5'-OH of the nucleoside, attacking the gamma phosphorous of ATP. Abstraction of the 5'-OH proton by Asp 35 activates the nucleophile, giving it the role of general base catalyst. The pentacoordinate transition state is stabilised by Lys 15 and Arg 126 side chains.
The phosphatase proceeds via a covalent phospho-aspartic acid and is dependent on magnesium for activity. Asp 165 acts as the nucleophile attacking the 3'-phosphorous in an SN2 phosphoryl transfer reaction.
Reaction

Catalytic Sites for 1ltq

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysA1515macie:sideChainStabilises the pentacoordinate transition state in the kinase reaction.
ArgA126126macie:sideChainStabilises the pentacoordinate transition state in the kinase.
AspA3535macie:sideChainGeneral base catalyst that activates the 5'-OH to increase its nucleophilicity, in the kinase domain.
AspA165165macie:sideChainNucleophile in the phosphatase, attacks the 3'-phosphorous in an SN2 phosphoryl transfer reaction.

Literature References

Notes:Magnesium is required in both reactions in stabilisation of the phosphate groups. In the case of ATP bound Mg, this is not included as strictly it is not a permanently bound group on the enzyme. Also, both enzyme activities are described in this annotation, although the PDB file displays only one EC code.
Wang LK
Structure and mechanism of T4 polynucleotide kinase: an RNA repair enzyme.
EMBO J 2002 21 3873-3880
PubMed: 12110598
Galburt EA
Structure of a tRNA repair enzyme and molecular biology workhorse: T4 polynucleotide kinase.
Structure 2002 10 1249-1260
PubMed: 12220496
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