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

P A Eistrikh-Heller,A G Gabdulkhakov,S V Rubinsky,M V Kovalchuk,A S Mironov,V R Samygina,A A Lashkov

doi:10.1134/s1063774521050059

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.

Highlights

In human cells, the demand for pyrimidine nitrogenous bases, in particular thymine and uridine, increases during the cancer disease development
High-quality crystals of uridine phosphorylase from the pathogenic bacterium Vibrio cholerae were grown in microgravity on board of the International Space Station (ISS)
Each subunit of the VchUPh molecule, which exists as a toroidal homohexamer with a diameter of ~106 Å, is composed of 253 residues

Summary

Introduction

The demand for pyrimidine nitrogenous bases, in particular thymine and uridine, increases during the cancer disease development. Nitrogenous bases are produced by the reversible phosphorolytic cleavage of pyrimidine nucleosides. This reaction is catalyzed by uridine phosphorylase (UPh). The expression of this protein is upregulated in cancer cells [1–3]. Some anticancer drugs are targeted to the regulation of metabolism of nitrogenous bases and their derivatives. UPh inhibitors can be used as such drugs. They regulate the metabolism of such nitrogenous bases as uridine and thymidine, the resynthesis of which involves UPh

Methods

Results

Conclusion