1R4F

Inosine-Adenosine-Guanosine Preferring Nucleoside Hydrolase From Trypanosoma vivax: Trp260Ala Mutant In Complex With 3-Deaza-Adenosine

Summary for 1R4F

• Entry DOI: 10.2210/pdb1r4f/pdb
• Related: 1HOZ 1HP0 1KIC 1KIE 1MAS 2MAS
• Descriptor: IAG-nucleoside hydrolase, CALCIUM ION, 3-DEAZA-ADENOSINE, ... (4 entities in total)
• Functional Keywords: rossmann fold, aromatic stacking, hydrolase
• Biological source: Trypanosoma vivax
• Total number of polymer chains: 2
• Total formula weight: 75554.11

Authors

Versees, W.,Loverix, S.,Vandemeulebroucke, A.,Geerlings, P.,Steyaert, J. (deposition date: 2003-10-06, release date: 2004-04-13, Last modification date: 2023-08-23)

Primary citation

Versees, W.,Loverix, S.,Vandemeulebroucke, A.,Geerlings, P.,Steyaert, J.
Leaving group activation by aromatic stacking: an alternative to general Acid catalysis.
J.Mol.Biol., 338:1-6, 2004

PubMed Abstract: General acid catalysis is a powerful and widely used strategy in enzymatic nucleophilic displacement reactions. For example, hydrolysis/phosphorolysis of the N-glycosidic bond in nucleosides and nucleotides commonly involves the protonation of the leaving nucleobase concomitant with nucleophilic attack. However, in the nucleoside hydrolase of the parasite Trypanosoma vivax, crystallographic and mutagenesis studies failed to identify a general acid. This enzyme binds the purine base of the substrate between the aromatic side-chains of Trp83 and Trp260. Here, we show via quantum chemical calculations that face-to-face stacking can raise the pKa of a heterocyclic aromatic compound by several units. Site-directed mutagenesis combined with substrate engineering demonstrates that Trp260 catalyzes the cleavage of the glycosidic bond by promoting the protonation of the purine base at N-7, hence functioning as an alternative to general acid catalysis.

PubMed: 15050818
DOI: 10.1016/j.jmb.2004.02.049

Experimental method

X-RAY DIFFRACTION (2.3 Å)