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Catalytic Site Atlas

CSA LITERATURE entry for 1a0i

E.C. nameDNA ligase (ATP)
SpeciesBacteriophage t7 (Virus)
E.C. Number (IntEnz)
CSA Homologues of 1a0i1fvi,1p8l,1x9n,2cfm,2hiv,2hix,2q2t,2q2u,3gde,
CSA Entries With UniProtID P00969
CSA Entries With EC Number
PDBe Entry 1a0i
PDBSum Entry 1a0i
MACiE Entry M0202

Literature Report

IntroductionDNA ligase is an essential enzyme required for the repair, replication and recombination of DNA. In all organisms except the prokaryotes it is dependent on the hydrolysis of ATP to AMP and pyrophosphate.
MechansimLys34 acts as a nucleophile and attacks the alpha-phosphate of ATP in a substitution reaction, liberating pyrophosphate and forming an intermediate covalently bound to the enzyme. The phosphate group of the first strand of DNA acts as a nucleophile and attacks the phosphate bound to Lys34 in a substitution reaction, liberating Lys34 and forming a DNA-AMP complex. The AMP phosphate deprotonates the hydroxyl group of the second DNA molecule, which then acts as a nucleophile and attacks the DNA phosphate of the DNA-AMP complex in a substitution reaction, liberating AMP and the ligated DNA.

Catalytic Sites for 1a0i

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysA3434macie:sideChainLys34 is the nucleophile in the first step of the reaction and is covalently attached to AMP until the final step.
LysA238238macie:sideChainStabilises transition states through reaction. May also position the pyrophosphate leaving group.
LysA240240macie:sideChainStabilises transition states through reaction.

Literature References

Odell M
Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining.
Mol Cell 2000 6 1183-1193
PubMed: 11106756
Tomkinson AE
Location of the active site for enzyme-adenylate formation in DNA ligases.
Proc Natl Acad Sci U S A 1991 88 400-404
PubMed: 1988940
Doherty AJ
Nick recognition by DNA ligases.
J Mol Biol 2000 296 43-56
PubMed: 10656817