Structural basis for the mechanism of inhibition of uridine phosphorylase from Salmonella typhimurium

X-ray structure ofSalmonella typhimuriumuridine phosphorylase complexed with 5-fluorouracil and molecular modelling of the complex of 5-fluorouracil with uridine phosphorylase fromVibrio cholerae

“…It may be hypothesized that Arg223 plays an important role in the conformational transitions of the L9 loop that are important for enzymatic function. Similar conformational changes of Arg223 have been detected in the complex of StUPh with its inhibitor 2,2 0 -anhydrouridine (Lashkov, Zhukhlistova, Sotnichenko et al, 2010), whereas in the hUPP1-5-FUra complex (Roosild et al, 2009;Roosild & Castronovo, 2010) the conformation of Arg275 (Arg223 in StUPh) remained unchanged.…”

“…The initial phase component of the structure factors for three-dimensional analysis of the StUPh-5-FUra complex was obtained by the molecular-replacement method using the program Phaser (McCoy et al, 2007). The B subunit of StUPh in complex with 2,2 0 -anhydrouridine previously refined to 1.86 Å resolution (Lashkov, Zhukhlistova, Sotnichenko et al, 2010; PDB entry 3fwp) was used as a starting atomic model. The atoms of the ligand and water molecules were removed from the starting model.…”

“…The conformation of the fragment containing residues 230-233 of L9 in StUPh (Fig. 1), as well as the respective fragment in EcUPh, is unstable (Lashkov, Zhukhlistova, Sotnichenko et al, 2010). The helix-to-loop transition, which depends on the presence or absence of the ligand in the catalytic centre, is critical for the enzymatic reaction.…”

“…Focusing on the structural aspects of pharmacological inhibition of UPh, we provided preliminary evidence about the spatial organization of the active centre of UPh from the pathogenic bacterium Salmonella typhimurium (StUPh) in a ligand-free state and in complexes with therapeutic agents (Lashkov, Zhukhlistova et al, 2009;Lashkov, Zhukhlistova, Sotnichenko et al, 2010). Here, we report the detailed X-ray analysis of the complex formed by 5-FUra with StUPh, as well as the molecular docking of 5-FUra into the X-ray structure of uridine phosphorylase from Vibrio cholerae (VchUPh).…”

Crystallization in Microgravity and the Atomic-Resolution Structure of Uridine Phosphorylase from Vibrio cholerae

“…Currently, great attention is given to the evaluation of the enzyme specificity of UPh and the development of reversible competitive inhibitors, the decrease in the concentration of which leads to the restoration of UPh activity. The structures of the protein from different organisms and its complexes with various ligands were determined and characterized at a resolution of up to 1.2 Å [4][5][6][7][8][9][10][11][12][13].…”