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Leaving group activation by aromatic stacking: an alternative to general acid catalysis
Wim Versées1, Stefan Loverix, An Vandemeulebroucke
1Laboratorium voor Ultrastructuur, Instituut voor Moleculaire Biologie, Vrije Universiteit Brussel and Vlaams Interuniversitair instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium. wversees@vub.ac.be
Journal of Molecular Biology
|March 31, 2004
Summary
Parasitic nucleoside hydrolase uses tryptophan instead of general acid catalysis. Tryptophan 260 protonates the purine base, enabling glycosidic bond cleavage and offering a novel enzymatic mechanism.
Area of Science:
- Biochemistry
- Enzymology
- Parasitology
Background:
- General acid catalysis is crucial for enzymatic nucleophilic displacement reactions, like N-glycosidic bond hydrolysis.
- The nucleoside hydrolase from Trypanosoma vivax lacks a general acid catalyst, despite its known function.
Purpose of the Study:
- To elucidate the catalytic mechanism of Trypanosoma vivax nucleoside hydrolase.
- To identify the role of tryptophan residues in the enzyme's active site.
Main Methods:
- Quantum chemical calculations to assess pKa changes of aromatic compounds.
- Site-directed mutagenesis to alter specific tryptophan residues.
- Substrate engineering to probe catalytic activity.
Main Results:
- Quantum chemical calculations revealed that face-to-face stacking of aromatic residues can significantly increase the pKa of heterocyclic compounds.
- Mutagenesis and substrate engineering identified Tryptophan 260 as the catalytic residue.
- Tryptophan 260 facilitates glycosidic bond cleavage by protonating the purine base at N-7.
Conclusions:
- Tryptophan 260 acts as an alternative to general acid catalysis in Trypanosoma vivax nucleoside hydrolase.
- This study reveals a novel catalytic mechanism involving aromatic residue interactions for enzymatic reactions.