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Catalytic Site Atlas

CSA LITERATURE entry for 1ako

E.C. nameexodeoxyribonuclease III
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz)
CSA Homologues of 1akoThere are 19 Homologs
CSA Entries With UniProtID P09030
CSA Entries With EC Number
PDBe Entry 1ako
PDBSum Entry 1ako
MACiE Entry M0160

Literature Report

IntroductionExonuclease III from E.coli is a multifunctional enzyme which is able to cleave DNA in order to facilitate the removal of a particular base to create an AP site. This process occurs during replication, allowing incorrectly placed base pairs to be removed and replaced by the correct one. The efficiency of this process is essential to protect E.coli from the damaging effects of mutations, and enables the fidelity of DNA polymerase activity to be increased by over 1000 times.
MechansimThe phosphodiester bond is cleaved at the 3' end to leave a free 3' OH group and a phosphorylated 5' end. This occurs through the nucleophilic attack of a water molecule, activated by deprotonation from His 259 which is itself primed through hydrogen bonding contacts with Asp 229. The bond formed between the water molecule and the phosphorous atom allows a pentavalent phosphate transition state to develop, stabilised by electrostatic contacts from a Mg2+ ion at the active site. This collapses to release the products and cleave the DNA backbone, following protonation of the 3' by Asp 151's side chain, which is primed by contacts with Asn 7 and Asn 153 to ensure that it is protonated at physiological pH.

Catalytic Sites for 1ako

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisA259259macie:sideChainDeprotonates the water molecule that attacks the electrophilic phosphorous atom to result in the cleavage of the phosphodiester bond.
AspA229229macie:sideChainActs to prime His 259 to allow it to act as an acid/base at physiological pH.
AsnA77macie:sideChainForms contacts to Asp 151 to ensure that it is protonated and can act as an acid.
AspA151151macie:sideChainActs as acid to protonate the leaving group.
AsnA153153macie:sideChainForms contacts to ensure that Asp 151 is protonated at physiological pH and can act as an acid.

Literature References

Notes:Mg 2+ is present at the active site but does not appear in the pdb file.
Kuo CF
Structure and function of the DNA repair enzyme exonuclease III from E. coli.
Ann N Y Acad Sci 1994 726 223-34
PubMed: 8092679