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

Abstract

Uridine phosphorylases are known as key targets for the development of new anticancer and antiparasitic agents. Crystals of uridine phosphorylase from the pathogenic bacterium Vibrio cholerae were grown in microgravity by the capillary counter-diffusion method on board of the International Space Station. The three-dimensional structure of this enzyme was determined at atomic (1.04 Å) resolution (RCSB PDB ID: 6Z9Z). Alternative conformations of long fragments (β-strands and adjacent loops) of the protein molecule were found for the first time in the three-dimensional structure of uridine phosphorylase in the absence of specific bound ligands. Apparently, these alternative conformations are related to the enzyme function. Conformational analysis with Markov state models demonstrated that conformational rearrangements can occur in the ligand-free state of the enzyme.

X-ray structure of Salmonella typhimurium uridine phosphorylase complexed with 5-fluorouracil and molecular modelling of the complex of 5-fluorouracil with uridine phosphorylase from Vibrio cholerae

Uridine phosphorylase (UPh), which is a key enzyme in the reutilization pathway of pyrimidine nucleoside metabolism, is a validated target for the treatment of infectious diseases and cancer. A detailed analysis of the interactions of UPh with the therapeutic ligand 5-fluorouracil (5-FUra) is important for the rational design of pharmacological inhibitors of these enzymes in prokaryotes and eukaryotes. Expanding on the preliminary analysis of the spatial organization of the active centre of UPh from the pathogenic bacterium Salmonella typhimurium (StUPh) in complex with 5-FUra [Lashkov et al. (2009), Acta Cryst. F65, 601-603], the X-ray structure of the StUPh-5-FUra complex was analysed at atomic resolution and an in silico model of the complex formed by the drug with UPh from Vibrio cholerae (VchUPh) was generated. These results should be considered in the design of selective inhibitors of UPhs from various species.