title: Glycal formation in crystals of uridine phosphorylase.
abstract: Uridine phosphorylase is a key enzyme in the pyrimidine salvage pathway. This enzyme catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate (or 2'-deoxyuridine to 2'-deoxyribose 1-phosphate). Here we report the structure of hexameric Escherichia coli uridine phosphorylase treated with 5-fluorouridine and sulfate and dimeric bovine uridine phosphorylase treated with 5-fluoro-2'-deoxyuridine or uridine, plus sulfate. In each case the electron density shows three separate species corresponding to the pyrimidine base, sulfate, and a ribosyl species, which can be modeled as a glycal. In the structures of the glycal complexes, the fluorouracil O2 atom is appropriately positioned to act as the base required for glycal formation via deprotonation at C2'. Crystals of bovine uridine phosphorylase treated with 2'-deoxyuridine and sulfate show intact nucleoside. NMR time course studies demonstrate that uridine phosphorylase can catalyze the hydrolysis of the fluorinated nucleosides in the absence of phosphate or sulfate, without the release of intermediates or enzyme inactivation. These results add a previously unencountered mechanistic motif to the body of information on glycal formation by enzymes catalyzing the cleavage of glycosyl bonds.
authors.affiliation: Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.
authors.forename: Debamita
authors.initials: D
authors.lastname: Paul
authors.forename: Seán E
authors.initials: SE
authors.lastname: O'Leary
authors.forename: Kanagalaghatta
authors.initials: K
authors.lastname: Rajashankar
authors.forename: Weiming
authors.initials: W
authors.lastname: Bu
authors.forename: Angela
authors.initials: A
authors.lastname: Toms
authors.forename: Ethan C
authors.initials: EC
authors.lastname: Settembre
authors.forename: Jennie M
authors.initials: JM
authors.lastname: Sanders
authors.forename: Tadhg P
authors.initials: TP
authors.lastname: Begley
authors.forename: Steven E
authors.initials: SE
authors.lastname: Ealick
mesh_terms: D020134:Catalytic Domain; D003001:Cloning, Molecular; D003460:Crystallization; D004926:Escherichia coli / Q000201:enzymology; D005467:Floxuridine / Q000494:pharmacology; D006801:Humans; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D013431:Sulfates / Q000494:pharmacology; D014461:Ultracentrifugation; D014529:Uridine / Q000494:pharmacology; D014543:Uridine Phosphorylase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D011994:Recombinant Proteins; D013431:Sulfates; D005467:Floxuridine; D014543:Uridine Phosphorylase; D014529:Uridine