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Catalytic Site Atlas

CSA LITERATURE entry for 1fr2

E.C. namedeoxyribonuclease I
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 3.1.21.1
CSA Homologues of 1fr2
CSA Entries With UniProtID
CSA Entries With EC Number 3.1.21.1
PDBe Entry 1fr2
PDBSum Entry 1fr2
MACiE Entry 1fr2

Literature Report

IntroductionColicin E9 from Escherichia coli is a non-specific endonuclease. This extracellular toxin is secreted by strains of E. coli to kill competing bacteria. It kills the cell by enzymatic cleavage of nucleic acids once it has entered the cell. Since colicin E9 is non-specific, it can hydrolyse both single and double stranded DNA.
Mechansim1. His 103 acts as a general base by abstracting a proton from a water molecule, activating it for nucleophilic attack on the scissile phosphorus atom. 2. The reaction goes by an SN2 mechanism, and proceeds through a negatively charged, penta-coordinate transition state, which is stabilised by a metal ion. 3. The P-O scissile bond is broken, and the 3' O atom of the leaving group is protonated by the positively charged His 102 residue. 4. The pKa of His 102 is raised by hydrogen bonding to Glu 100. 5. Arg 5 stabilises the product 5' phosphate.

Catalytic Sites for 1fr2

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisB102550macie:sideChainActs as a general acid by protonating the leaving group 3' O atom.
HisB103551macie:sideChainActs as a general base by deprotonating a water molecule, activating it for nucleophilic attack on the phosphorus atom.
GluB100548macie:sideChainHydrogen bonds to His 102, raising its pKa and facilitating the protonation of the 3' O leaving group.
ArgB5453macie:sideChainStabilises the product 5' phosphate.

Literature References

Notes:
Pommer AJ
Mechanism and cleavage specificity of the H-N-H endonuclease colicin E9.
J Mol Biol 2001 314 735-749
PubMed: 11733993
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