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Catalytic Site Atlas

CSA LITERATURE entry for 1avq

E.C. nameexodeoxyribonuclease (lambda-induced)
SpeciesBacteriophage lambda ()
E.C. Number (IntEnz) 3.1.11.3
CSA Homologues of 1avq
CSA Entries With UniProtID P03697
CSA Entries With EC Number 3.1.11.3
PDBe Entry 1avq
PDBSum Entry 1avq
MACiE Entry 1avq

Literature Report

IntroductionLambda-exonuclease from Bacteriophage lambda is a 5'->3' exonuclease. It catalyses the hydrolysis of one strand of double stranded DNA in a 5' to 3' direction, leaving single stranded DNA. This is involved in DNA replication, recombination and repair. Once started on a reaction, lambda-exonuclease will continue to hydrolyse until either the DNA strand ends, or the enzyme dissociates into monomers.
MechansimThe three-metal mechanism of EcoRV is the most likely mechanism for lambda-exonuclease.
1. Metal I and Lys 131 between them activate a water molecule for nucleophilic attack on the scissile phosphate. 2. Nucleophilic attack creates a negatively charged, penta-coordinate transition state, which is stabilised by metal III. 3. The 3' O atom of the leaving group of the SN2 reaction is protonated by a water molecule. The resulting hydroxide is stabilised by metal III.
Reaction

Catalytic Sites for 1avq

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysA131131macie:sideChainActivates a water molecule for nucleophilic attack on the scissile phosphate.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysB131131macie:sideChainActivates a water molecule for nucleophilic attack on the scissile phosphate.

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysC131131macie:sideChainActivates a water molecule for nucleophilic attack on the scissile phosphate.

Literature References

Notes:The mechanism proposed here is based purely on lambda-exonuclease's homology to EcoRV (stated in 9653111.) Metals I, II and III are not in the crystallised structure of lambda-exonuclease 1avq. Residues Asp 119 and Glu 129 are stated to be catalytic, but seem to only be necessary for binding.
Kovall RA
Type II restriction endonucleases: structural, functional and evolutionary relationships.
Curr Opin Chem Biol 1999 3 578-583
PubMed: 10508668
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