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Search The CSA
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Catalytic Site Atlas

CSA LITERATURE entry for 1a79

E.C. nametRNA-intron endonuclease
SpeciesMethanococcus jannaschii ()
E.C. Number (IntEnz) 3.1.27.9
CSA Homologues of 1a791r0v,1r11,1rlv,2cv8,2gjw,2ohc,2ohe,2zyz,3iey,
CSA Entries With UniProtID Q58819
CSA Entries With EC Number 3.1.27.9
PDBe Entry 1a79
PDBSum Entry 1a79
MACiE Entry 1a79

Literature Report

IntroductionRNA endonuclease from the archaea M. jannaschii is able to catalyse the splicing of introns from tRNA, a process needed only in archaea and eukarya, bacterial tRNA introns being self-splicing. The enzyme thus is a homologue of the eukaryotic enzymes which perform, a fact that serves to reinforce the closer relationship proposed between archaea and eukarya. There are differences however in the exact orientation of residues at the active site and the substrate recognition by the enzymes, suggesting that the enzymes evolved from a common ancestor with slightly different function.
MechansimThe overall reaction catalysed by the endonuclease is the formation of a 5'OH and a 2'3'cyclic phosphate, thus cleaving the RNA. This occurs through nucleophilic attack by the 3'OH on the phosphate facilitated by deprotonation by His 125, which dissociates from the 5' via protonation by Tyr 115 via a pentavalent phosphate transition state stabilised by Lys 156.
Reaction

Catalytic Sites for 1a79

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysA156156macie:sideChainStabilises the pentavalent phosphate that forms in the reaction through electrostatic interactions.
TyrA115115macie:sideChainProtonates the 5' Oxygen to allow it to act as a leaving group in the reaction thus facilitating an SN2 displacement at the electrophilic phosphorous centre.
HisA125125macie:sideChainDeprotonates the 3'OH group to allow it to act as a nucleophile and attack the electrophilic phosphorous forming the pentavalent phosphate transition state.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysB156156macie:sideChainStabilises the pentavalent phosphate that forms in the reaction through electrostatic interactions.
TyrB115115macie:sideChainProtonates the 5' Oxygen to allow it to act as a leaving group in the reaction thus facilitating an SN2 displacement at the electrophilic phosphorous centre.
HisB125125macie:sideChainDeprotonates the 3'OH group to allow it to act as a nucleophile and attack the electrophilic phosphorous forming the pentavalent phosphate transition state.

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysC156156macie:sideChainStabilises the pentavalent phosphate that forms in the reaction through electrostatic interactions.
TyrC115115macie:sideChainProtonates the 5' Oxygen to allow it to act as a leaving group in the reaction thus facilitating an SN2 displacement at the electrophilic phosphorous centre.
HisC125125macie:sideChainDeprotonates the 3'OH group to allow it to act as a nucleophile and attack the electrophilic phosphorous forming the pentavalent phosphate transition state.

Annotated By Reference To The Literature - Site 4 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysD156156macie:sideChainStabilises the pentavalent phosphate that forms in the reaction through electrostatic interactions.
TyrD115115macie:sideChainProtonates the 5' Oxygen to allow it to act as a leaving group in the reaction thus facilitating an SN2 displacement at the electrophilic phosphorous centre.
HisD125125macie:sideChainDeprotonates the 3'OH group to allow it to act as a nucleophile and attack the electrophilic phosphorous forming the pentavalent phosphate transition state.

Literature References

Notes:
Li H
Crystal structure and evolution of a transfer RNA splicing enzyme.
Science 1998 280 279-284
PubMed: 9535656
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