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Catalytic Site Atlas Search Results
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Catalytic Site Atlas

CSA LITERATURE entry for 1cz0

E.C. nameDNA (5'- D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*T *CP*A)-3')
SpeciesPhysarum polycephalum (Slime mold)
E.C. Number (IntEnz) 3.1.-.-
CSA Homologues of 1cz0
CSA Entries With UniProtID
CSA Entries With EC Number 3.1.-.-
PDBe Entry 1cz0
PDBSum Entry 1cz0
MACiE Entry 1cz0

Literature Report

IntroductionI-PpoI is a homing endonuclease of the His-Cys family. It is encoded by the nuclear 26S rRNA gene of Physarum polycephalum and cleaves a 16 bp homing site to generate four-base 3' overhangs. It requires divalent metal cations, but a wide range are accommodated.
Mechansim1) The metal (likely to be magnesium in the native enzyme) is bound by Asn 119, a non-bridging oxygen of the scissile phosphate group, and the bridging 3' oxygen of the scissile bond. Mg(II) forces the DNA into a strained conformation.
2) A water molecule, activated by His 98 acting as a base, performs inline attack on the scissile phosphate. The backbone of Cys 105 may increase the pKa of His 98 by hydrogen bonding to the protonated nitrogen of His 98.
3) Mg(II) and His 98 stabilise the charge on the pentacovalent transition state.
4) The transition state collapses with the 3' hydroxylate leaving group being stabilised by Mg(II) and Arg 61.
5) Mg(II) acidifies a bound water molecule which can then donate a proton to the 3' hydroxylate product.

Catalytic Sites for 1cz0

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisA9898macie:sideChainHis 98 activates the water molecule which performs nucleophilic, inline attack on the scissile phosphate group.
His 98 also stabilises the charge build-up in the transition state.
ArgA6161macie:sideChainArg 61 appears to stabilise the cleavage products, driving equilibrium over to the product side and preventing religation.
CysA105105macie:mainChainCarbonylThe main chain carbonyl of Cys 105 hydrogen bonds to His 98, increasing the pKa of His 98.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisB29898macie:sideChainHis 98 activates the water molecule which performs nucleophilic, inline attack on the scissile phosphate group.
His 98 also stabilises the charge build-up in the transition state.
CysB305105macie:mainChainCarbonylThe main chain carbonyl of Cys 105 hydrogen bonds to His 98, increasing the pKa of His 98.
ArgB26161macie:sideChainArg 61 appears to stabilise the cleavage products, driving equilibrium over to the product side and preventing religation.

Literature References

Notes:
Galburt EA
A novel endonuclease mechanism directly visualized for I-PpoI.
Nat Struct Biol 1999 6 1096-1099
PubMed: 10581547
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