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Catalytic Site Atlas

CSA LITERATURE entry for 1znv

E.C. nameCOLICIN E7 IMMUNITY PROTEIN
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 3.1.-.-
CSA Homologues of 1znv
CSA Entries With UniProtID
CSA Entries With EC Number 3.1.-.-
PDBe Entry 1znv
PDBSum Entry 1znv
MACiE Entry 1znv

Literature Report

IntroductionThe ColE7 endonuclease from Escherichia coli binds nucleic acids and hydrolyzes a phosphodiester bond. It contains the His-metal finger motif and may function with a range of metals, although the physiological metal is thought to be Zn(II).
Mechansim1) A water nucleophile is polarised by His 545, which acts as a general base to generate hydroxide.
2) An non-bridging oxygen of the scissile phosphodiester group coordinates to Zn(II), making the phosphorus more electrophilic.
3) Hydroxide attacks the scissile phosphodiester bond.
4) Zn(II) stabilises the charge build-up in the pentacovalent transition state.
5) The transition state collapses, with Zn(II) stabilising the charge on the terminal 3' hydroxyl cleavage product.

Catalytic Sites for 1znv

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluB545545macie:sideChainHis 545 acts as the general base catalyst, deprotonating water as it attacks as a nucleophile.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluD545545macie:sideChainHis 545 acts as the general base catalyst, deprotonating water as it attacks as a nucleophile.

Literature References

Notes:The literature does not state if His 545 is the acid that protonates the 3' hydroxy cleavage product.
Doudeva LG
Crystal structural analysis and metal-dependent stability and activity studies of the ColE7 endonuclease domain in complex with DNA/Zn2+ or inhibitor/Ni2+.
Protein Sci 2006 15 269-280
PubMed: 16434744
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