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Catalytic Site Atlas

CSA LITERATURE entry for 1jch

E.C. nameCOLICIN E3
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 3.1.21.-
CSA Homologues of 1jch1e44,2b5u,
CSA Entries With UniProtID
CSA Entries With EC Number 3.1.21.-
PDBe Entry 1jch
PDBSum Entry 1jch
MACiE Entry 1jch

Literature Report

IntroductionColicin E3 kills E.coli cells by binding to a surface receptor, entering the cell and inactivating protein biosynthetic machinery by ribonucleolytic cleavage of the ribosomal subunit 16S rRNA.
The mechanism shows homology to ribonuclease T1.
MechansimThe mechanism of colicin E3 involves a Glu-His-Asp catalytic triad. The carboxylate of Glu 517 acts as a general base catalyst to abstract a proton from the ribose O2'-hydroxyl of adenine 1493 of the ribosomal subunit. This increases the nucleophilicity of the oxygen atom so that it makes a nucleophilic attack on the phosphate to form a cyclic 2'-3' phosphate with a negative charge. The pentacoordinate cyclic phosphate intermediate is stabilised by Arg 545. Asp 510 activates His 513 to enable it to act as a general acid catalyst to facilitate loss of the leaving group by donation of a proton to the leaving 5'-OH RNA fragment upon cleavage. His 513 then acts as a general base catalyst to activate a water molecule for nucleophilic attack on the phosphorous atom of the 2'-3' cyclic phosphate. Glu 517 acts as a general acid catalyst to donate its proton to the O2' atom.

Catalytic Sites for 1jch

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspA510510macie:sideChainActivates His 513.
HisA513513macie:sideChainFunctions as a general acid/base catalyst to promote scissile bond cleavage and activation of water as a nucleophile.
ArgA545545macie:sideChainStabilises the pentacoordinate cyclic phosphate intermediate.
GluA517517macie:sideChainActs as a general acid/base catalyst to activate the ribose O2' oxygen to act as a nucleophile, and protonate the same oxygen again after cleavage.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspC510510macie:sideChainActivates His 513.
HisC513513macie:sideChainFunctions as a general acid/base catalyst to promote scissile bond cleavage and activation of water as a nucleophile.
ArgC545545macie:sideChainStabilises the pentacoordinate cyclic phosphate intermediate.
GluC517517macie:sideChainActs as a general acid/base catalyst to activate the ribose O2' oxygen to act as a nucleophile, and protonate the same oxygen again after cleavage.

Literature References

Notes:
Zarivach R
On the interaction of colicin E3 with the ribosome.
Biochimie 2002 84 447-454
PubMed: 12423788
Soelaiman S
Crystal structure of colicin E3: implications for cell entry and ribosome inactivation.
Mol Cell 2001 8 1053-1062
PubMed: 11741540
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