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

Abstract

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.

Expression, purification, crystallization and preliminary X-ray structure analysis ofVibrio choleraeuridine phosphorylase in complex with thymidine

“…The activity of UPh is known to be vital in some pathogenic bacteria and protozoa (Jimé nez et al, 1989;Lee et al, 1988). In previous publications, we have reported structures of UPh from Salmonella typhimurium with physiological ligands and pharmacological inhibitors (Dontsova et al, 2004(Dontsova et al, , 2005Timofeev et al, 2007;Lashkov et al, 2009Lashkov et al, , 2010Lashkov et al, , 2012. However, the diffraction resolution of complexes of bacterial UPh with thymidine does not allow conclusions to be drawn regarding the details of enzyme-ligand binding.…”

Structural Insights into the Quaternary Catalytic Mechanism of Hexameric Human Quinolinate Phosphoribosyltransferase, a Key Enzyme in de novo NAD Biosynthesis

“…Although the apo structure of Hs QPRT showed dynamic movement between the open and closed conformations in its active site and its dimer-dimer interface, it can exist as a hexamer through extensive hydrophobic contacts with helix α1. Some pentosyltransferases (EC 2.4.2) adopt a hexameric configuration through the trimerisation of dimers, such as nucleoside phosphorylases (PDB codes 4E1V, 4D8Y and 4R2X) 35 36 37 ; however, it is unusual for the short α helix of Hs QPRT to contribute to hexamer stability while its flexible loops show dynamic conformational changes. First, loops L and O of Hs QPRT were closed upon QA binding.…”

Binding Pattern and Structural Interactome of the Anticancer Drug 5-Fluorouracil: A Critical Review

“…Given its pivotal role in 5-FU-based chemotherapy, uridine phosphorylase is an attractive target for drug development. Crystal structures of uridine phosphorylase complexed with 5-FU are available from various sources, including Escherichia coli (PDB ID 1RXC and 3KVV) [ 35 , 36 ], bovine Bos taurus (PDB ID 3KVR) [ 35 ], Homo sapiens (PDB ID 3NBQ) [ 37 ], Salmonella typhimurium (PDB ID 4E1V) [ 38 ], and Schistosoma mansoni (PDB ID 4TXN) [ 39 ]. The amino acid sequence of uridine phosphorylase is conserved across prokaryotes and eukaryotes ( Table 4 ).…”