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Catalytic Site Atlas

CSA LITERATURE entry for 1vas

E.C. namedeoxyribonuclease (pyrimidine dimer)
SpeciesBacteriophage t4 (Virus)
E.C. Number (IntEnz) 3.1.25.1
CSA Homologues of 1vas1end,1eni,1enj,1enk,2end,2fcc,
CSA Entries With UniProtID P04418
CSA Entries With EC Number 3.1.25.1
PDBe Entry 1vas
PDBSum Entry 1vas
MACiE Entry M0162

Literature Report

IntroductionEndonuclease V removes pyrimidine dimers in DNA induced by UV radiation. The enzyme first associates with the DNA and locates the damaged site by a scanning mechanism. It catalyses 2 reactions to remove DNA pyrimidine dimers: (1)cleavage of glycosidic bond by pyrimidine dimer glycosylase activity, which hydrolyses the N-glycosyl bond of the 5'-thymidine in the thymine dimer site and (2)incision of the phosphodiester bond at the apyrimidinic site via a beta-elimination reaction by the apurinic/apyrimidinic(AP) endonuclease activity.
MechansimThe glycosylase step proceeds by an SN2 mechanism. The neutral N-terminus(Thr2) performs a nucleophilic attack on ribose C1' of the 5'-thymine of the dimer. The susceptibility of C1' to nucleophilic attack is enhanced by a hydrogen bond between Glu23 and O4' of the ribose. The transition state is stabilised by the hydrogen bond as well. The positively charged Arg22 and Arg26 provides favourable electrostatic interactions to the transition state and hence stabilising it. Glu23 protonates ribose O4', leading to the opening of the ribose ring and the formation of the protonated Schiff base, the product of the glycosylase reaction, which is stabilised by Glu23.
The AP endonuclease step proceeds via a beta-elimination mechanism. Glu23 acts as a base to remove the pro-S 2'-hydrogen of the opened ribose, leading to the cleavage of the phosphodiester bond. It is followed by the hydrolysis of the Schiff base by a water molecule, leading to the dissociation of the enzyme and the formation of an alpha-beta-unsaturated aldehyde.

Catalytic Sites for 1vas

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ArgA2222macie:sideChainIt stabilises the transition state of the glycosylase reaction by forming favourable electrostatic interaction.
ThrA22macie:mainChainAmideThe N-terminal of Thr 2 acts as a nucleophile to attack the ribose C1' of the 5'-thymine of the dimer.
GlnA2323macie:sideChainIn the glycosylase reaction, it hydrogen bonds to ribose O4' to increase the electrophilicity of ribose C1' to enhance the nucleophilic attack of Thr 2 on C1' The hydrogen bond stabilises the transition state as well. It protonates the ribose O4', leading to the opening of the ribose ring and the formation of the Schiff base, which is stabilised again by Glu 23. In the AP endonuclease reaction, it acts as a base to remove the pro-S 2'-hydrogen of the opened ribose, leading to the cleavage of the phosphodiester bond.
ArgA2626macie:sideChainIt stabilises the transition state in the glycosylase reaction by providing favourable electrostatic interaction.

Literature References

Notes:
Schrock RD 3rd
Site-directed mutagenesis of the NH2 terminus of T4 endonuclease V. The position of the alpha NH2 moiety affects catalytic activity.
J Biol Chem 1993 268 880-886
PubMed: 8419366
Doi T
Role of the basic amino acid cluster and Glu-23 in pyrimidine dimer glycosylase activity of T4 endonuclease V.
Proc Natl Acad Sci U S A 1992 89 9420-9424
PubMed: 1409651
Morikawa K
X-ray structure of T4 endonuclease V: an excision repair enzyme specific for a pyrimidine dimer.
Science 1992 256 523-526
PubMed: 1575827
Fuxreiter M
Role of active site residues in the glycosylase step of T4 endonuclease V. Computer simulation studies on ionization states.
Biochemistry 1999 38 9577-9589
PubMed: 10423235
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