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Catalytic Site Atlas

CSA LITERATURE entry for 1pyl

E.C. name
SpeciesStreptomyces aureofaciens (Bacteria)
E.C. Number (IntEnz) 3.1.4.8
CSA Homologues of 1pyl
CSA Entries With UniProtID
CSA Entries With EC Number 3.1.4.8
PDBe Entry 1pyl
PDBSum Entry 1pyl
MACiE Entry 1pyl

Literature Report

IntroductionThree different strains of Streptomyces aureofaciens produce the homologous ribonucleases Sa, Sa2 and Sa3. They are all guanylate endoribonucleases, highly specifically hydrolysing the phosphodiester bonds of RNA at the 3'-side of guanosine nucleotides. These enzymes belong to the prokaryotic subgroup of microbial ribonucleases, and are some of the smallest enzymes known.
MechansimThe mechanism is acid-base catalysis of the RNA self-cleavage reaction, with transition state stabilisation:
1) The 2' hydroxyl group of the substrate is made more nucleophilic by deprotonation by Glu 56.
2) The 2' hydroxyl attacks the phosphorus attached to the 3' carbon of the same ribose ring, displacing the 5' oxygen of the next nucleotide. The charge on the trigonal bipyramidal transition state is stabilised by Arg 67.
3) The 5' oxygen of the next nucleotide is made a better leaving group by protonation by His 86.
The product is a cyclophosphodiester between the 3' and 2' carbons of the guanosine nucleotide. This is hydrolysed in the second step of the reaction, which is the reverse of the first step with water as the nucleophile, displacing the 2' hydroxyl. His 86 activates water by deprotonation and Glu 56 protonates the 2' hydroxyl leaving group. Arg 67 stabilises the transition state.
Reaction

Catalytic Sites for 1pyl

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluA56122macie:sideChainGlu 56 deprotonates the substrate 2' hydroxyl nucleophile in the first step, and reprotonates the 2' hydroxyl leaving group in the second step of the reaction.
HisA86152macie:sideChainHis 86 protonates the 5' leaving group in the first step and deprotonates water in the second step of the reaction.
ArgA67133macie:sideChainArg 67 stabilises the trigonal bipyramid geometry and negative charge of the transition states.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluB56122macie:sideChainGlu 56 deprotonates the substrate 2' hydroxyl nucleophile in the first step, and reprotonates the 2' hydroxyl leaving group in the second step of the reaction.
HisB86152macie:sideChainHis 86 protonates the 5' leaving group in the first step and deprotonates water in the second step of the reaction.
ArgB67133macie:sideChainArg 67 stabilises the trigonal bipyramid geometry and negative charge of the transition states.

Literature References

Notes:
Sevcík J
Crystal structure reveals two alternative conformations in the active site of ribonuclease Sa2.
Acta Crystallogr D Biol Crystallogr 2004 60 1198-1204
PubMed: 15213380
Yakovlev GI
Contribution of active site residues to the activity and thermal stability of ribonuclease Sa.
Protein Sci 2003 12 2367-2373
PubMed: 14500895
Takahashi K
Ribonuclease T1, Structure and function.
Adv Biophys 1970 1 53-98
PubMed: 4364371
Sevcik J
Complex of ribonuclease Sa with a cyclic nucleotide and a proposed model for the reaction intermediate.
Eur J Biochem 1993 216 301-305
PubMed: 8396032
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