Preliminary investigation of the three-dimensional structure ofSalmonella typhimuriumuridine phosphorylase in the crystalline state

Abstract

PDB Reference: StUPh, 1sj9, r1sj9sf.Uridine phosphorylase (UPh) catalyzes the phosphorolytic cleavage of the C-N glycosidic bond of uridine to ribose 1-phosphate and uracil in the pyrimidine-salvage pathway. The crystal structure of the Salmonella typhimurium uridine phosphorylase (StUPh) has been determined at 2.5 Å resolution and refined to an R factor of 22.1% and an R free of 27.9%. The hexameric StUPh displays 32 point-group symmetry and utilizes both twofold and threefold non-crystallographic axes. A phosphate is bound at the active site and forms hydrogen bonds to Arg91, Arg30, Thr94 and Gly26 of one monomer and Arg48 of an adjacent monomer. The hexameric StUPh model reveals a close structural relationship to Escherichia coli uridine phosphorylase (EcUPh).

Glycal Formation in Crystals of Uridine Phosphorylase,

“…The structure of Salmonella typhimurium UP is very similar to that of EcUP (5). The bacterial enzyme exists as a hexamer comprised of six identical subunits.…”

A novel structural mechanism for redox regulation of uridine phosphorylase 2 activity

“…Our understanding of the fundamental catalytic mechanisms underlying UPP activity was founded on the structural analysis of bacterial UPPs, first with E. coli UPP (Morgunova et al, 1995; Burling et al, 2003; Caradoc-Davies et al, 2004; Bu et al, 2005) followed by research on the closely-related S. typhimurium homologue (Dontsova et al, 2005; Lashkov et al, 2009, 2010). Only recently have multiple structures of the human enzyme, hUPP1 (Roosild et al, 2009; Roosild and Castronovo, 2010), its bovine homologue, bUPP1 (Paul et al, 2010), and a UPP from the parasitic protozoa, Trypanosoma brucei (Larson et al, 2010), revealed key differences between prokaryotic and eukaryotic variations of this enzyme.…”

Isolation, crystallization and preliminary crystallographic analysis ofSalmonella typhimuriumuridine phosphorylase crystallized with 2,2′-anhydrouridine

“…The space group and unit-cell parameters of these crystals (Table 1) are strikingly different from those of the native (Dontsova et al, 2005; space group P6 1 ; a = 91.37, c = 266.38 Å ), despite the fact that the native crystals were obtained under similar conditions with a reservoir solution consisting of 100 mM sodium acetate pH 5.0, 7%(w/v) PEG 8000. We anticipate that the structure determination in progress will reveal that these are crystals of the complex of StUPh with ANU.…”

“…The structure was solved by molecular replacement. The previously reported hexamer structure of S. typhimurium uridine phosphorylase at 2.5 Å resolution (Dontsova et al, 2005; PDB code 1sj9) was used as the starting model. The amino-acid sequence was obtained from the SWISS-PROT database (CAA74658).…”

“…The crystal structure of the native S. typhimurium uridine phosphorylase (StUPh) has been determined previously (Dontsova et al, 2005) and found to be hexameric. Here, we describe the preparation of new crystal form of the enzyme grown in the presence of the ligand 2,2 0 -anhydrouridine (ANU).…”