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Catalytic Site Atlas

CSA LITERATURE entry for 1f8x

E.C. namenucleoside deoxyribosyltransferase
SpeciesLactobacillus leichmannii (Bacteria)
E.C. Number (IntEnz)
CSA Homologues of 1f8xThere are 12 Homologs
CSA Entries With UniProtID Q9R5V5
CSA Entries With EC Number
PDBe Entry 1f8x
PDBSum Entry 1f8x
MACiE Entry 1f8x

Literature Report

IntroductionNucleoside 2'-deoxyribosyltransferase catalyses cleavage of the 2'-deoxyribosyl-nucleoside glycosidic bond through the formation of a covalent deoxyribosyl-enzyme intermediate. The enzyme is found in various Lactobacilli species where it participates in nucleoside recycling.
MechansimThe mechanism is thought the proceed via double displacement, resulting in retention of stereochemical configuration in the product. The catalytic nucleophile Glu98 attacks at the scissile glycosidic bond of 2'-deoxyribos-nucleoside, forming an enzyme-substrate intermediate which then collapses on attack by the second base, forming a new deoxyribosyl nucleoside. Asp92 is thought to act as a general acid to the departing glycosidic oxygen while Asp72 stabilises the oxo-carbenium character transition state.

Catalytic Sites for 1f8x

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluA9898macie:sideChainThe residue acts as a nucleophile towards the substrate glycosidic link in an overall double inversion attack. It is positioned for catalysis by hydrogen bonding to the close proximity Tyr7.
AspA9292macie:sideChainThe residue is thought to act as a general acid to the glycosidic oxygen of the cleaved bond.
AspA7272macie:sideChainThe reside acts to stabilise the oxo-carbenium ion transition state.
TyrA77macie:sideChainThe phenolic oxygen of the residue hydrogen bonds to the nucleophilic Glu98, orientating it towards the substrate in catalysis.

Literature References

Armstrong SR
Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site.
Structure 1996 4 97-107
PubMed: 8805514
Short SA
Active site amino acids that participate in the catalytic mechanism of nucleoside 2'-deoxyribosyltransferase.
J Biol Chem 1996 271 4978-4987
PubMed: 8617773
Porter DJ
Identification of the active site nucleophile in nucleoside 2-deoxyribosyltransferase as glutamic acid 98.
J Biol Chem 1995 270 15551-15556
PubMed: 7797550