ABSTRACT
Pyrimidine-nucleoside phosphorylase catalyzes the phosphorolytic cleavage of thymidine and uridine with equal activity. Investigation of this protein is essential for anticancer drug design. Here, the structure of this protein from Bacillus subtilis in complex with imidazole and sulfate is reported at 1.9â Å resolution, which is an improvement on the previously reported structure at 2.6â Å resolution. The localization and position of imidazole in the nucleoside-binding site reflects the possible binding of ligands that possess an imidazole ring.
Subject(s)
Bacillus subtilis/enzymology , Imidazoles/metabolism , Pyrimidine Phosphorylases/chemistry , Pyrimidine Phosphorylases/metabolism , Sulfates/metabolism , Amino Acid Sequence , Binding Sites , Catalytic Domain , Crystallization , Crystallography, X-Ray , Imidazoles/chemistry , Models, Molecular , Protein Conformation , Substrate Specificity , Sulfates/chemistryABSTRACT
Uridine phosphorylase (UPh; EC 2.4.2.3) catalyzes the phosphorolytic cleavage of the N-glycosidic bond of uridine to form ribose 1-phosphate and uracil. This enzyme also activates pyrimidine-containing drugs, including 5-fluorouracil (5-FU). In order to better understand the mechanism of the enzyme-drug interaction, the complex of Salmonella typhimurium UPh with 5-FU was cocrystallized using the hanging-drop vapour-diffusion method at 294 K. X-ray diffraction data were collected to 2.2 A resolution. Analysis of these data revealed that the crystal belonged to space group C2, with unit-cell parameters a = 158.26, b = 93.04, c = 149.87 A, alpha = gamma = 90, beta = 90.65 degrees . The solvent content was 45.85% assuming the presence of six hexameric molecules of the complex in the unit cell.
Subject(s)
Antimetabolites, Antineoplastic/metabolism , Fluorouracil/metabolism , Uridine Phosphorylase/analysis , Uridine Phosphorylase/metabolism , X-Ray Diffraction , Binding Sites , Crystallization , Data Collection , Escherichia coli/genetics , Models, Molecular , Plasmids , Protein Binding , Salmonella typhimurium/enzymology , Statistics as Topic , Temperature , Transformation, Bacterial , Uridine Phosphorylase/chemistry , Uridine Phosphorylase/isolation & purification , Water/metabolismABSTRACT
The electrophile Ca(2+) is an essential multifunctional co-factor in the phospholipase A(2) mediated hydrolysis of phospholipids. Crystal structures of an acidic phospholipase A(2) from the venom of Bothrops jararacussu have been determined both in the Ca(2+) free and bound states at 0.97 and 1.60 A resolutions, respectively. In the Ca(2+) bound state, the Ca(2+) ion is penta-coordinated by a distorted pyramidal cage of oxygen and nitrogen atoms that is significantly different to that observed in structures of other Group I/II phospholipases A(2). In the absence of Ca(2+), a water molecule occupies the position of the Ca(2+) ion and the side chain of Asp49 and the calcium-binding loop adopts a different conformation.