Literature summary for 2.4.2.3 extracted from

Prokofev, I.; Lashkov, A.; Gabdulkhakov, A.; Balaev, V.; Seregina, T.; Mironov, A.; Betzel, C.; Mikhailov, A.
X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion substrate specificity of bacterial uridine phosphorylases (2016), Crystallogr. Rep., 61, 954-973 .

No PubMed abstract available

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified native enzyme uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion, hanging drop vapor diffusion technique, mixing of 0.002 ml of 15 mg/ml protein in 20 mM Tris-HCl, pH 7.5, 20 mM NaCl, and ligand, with 0.002 ml of reservoir solution containing 0.2 M MgCl2 hexahydrate, 15% w/v PEG 4000, 0.1 M Tris-HCl, pH 8.5, and with 0.001 ml of 0.1 M thymidine solution, for the enzyme-phosphate complex, sitting drop vapour diffusion method is used mixing 0.001 ml of the same protein solution with 0.001 ml of reservoir solution containing 0.5 M sodium diphosphate, 0.1 M ammonium sulfate, and 0.5 M potassium diphosphate, pH 7.5, 1 week, 18°C, X-ray diffraction structure determiantion and analysis at 1.29-2.24 A resolution, modeling	Vibrio cholerae

Crystallization (Comment)

Organism

purified native enzyme uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion, hanging drop vapor diffusion technique, mixing of 0.002 ml of 15 mg/ml protein in 20 mM Tris-HCl, pH 7.5, 20 mM NaCl, and ligand, with 0.002 ml of reservoir solution containing 0.2 M MgCl2 hexahydrate, 15% w/v PEG 4000, 0.1 M Tris-HCl, pH 8.5, and with 0.001 ml of 0.1 M thymidine solution, for the enzyme-phosphate complex, sitting drop vapour diffusion method is used mixing 0.001 ml of the same protein solution with 0.001 ml of reservoir solution containing 0.5 M sodium diphosphate, 0.1 M ammonium sulfate, and 0.5 M potassium diphosphate, pH 7.5, 1 week, 18°C, X-ray diffraction structure determiantion and analysis at 1.29-2.24 A resolution, modeling

Vibrio cholerae

Organism

Organism	UniProt	Comment	Textmining
Vibrio cholerae	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
native enzyme by hydrophobic interaction and anion exchange chromatography, to homogeneity	Vibrio cholerae

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
additional information	substrate specificity, and substrate binding structures, detailed overview	Vibrio cholerae	?	-	-

Subunits

Subunits	Comment	Organism
homohexamer	6 * 27500, SDS-PAGE	Vibrio cholerae
More	spatial organization of the AB homodimer of the VchUPh complex containing thymidine (THM) at the enzyme active site and a sodium ion (Na+) at the intersubunit interface. Hydrophobic residues are distributed throughout the subunit and play a key role in the formation of the structural core of the molecule. Detailed enzyme structure analysis, overview	Vibrio cholerae

Synonyms

Synonyms	Comment	Organism
VchUPh	-	Vibrio cholerae

General Information

General Information	Comment	Organism
additional information	the formation of a hydrogen-bond network between the 2'-hydroxy group of uridine and atoms of the active-site residues of uridine phosphorylase leads to conformational changes of the ribose moiety of uridine, resulting in an increase in the reactivity of uridine compared to thymidine. Since the binding of thymidine to residues of uridine phosphorylase causes a smaller local strain of the beta-N1-glycosidic bond in this the substrate compared to the uridine molecule, the beta-N1-glycosidic bond in thymidine is more stable and less reactive than that in uridine. The phosphate anion, which is the second substrate bound at the active site, interacts simultaneously with the residues of the beta5-strand and the beta1-strand through hydrogen bonding, thus securing the gate loop in a conformation so that the active site of the enzyme molecule becomes inaccessible for nucleoside binding. Structures of VchUPh in complexes with thymine and uracil are prepared for molecular docking of the second substrates of the reverse reaction (ribose 1-phosphate and 2-deoxyribose 1-phosphate). The phosphate-binding F site of the EF homodimer of VchUPh is formed by hydrophilic residues, four of which belong to the F subunit (Thr93/F, Gly25/F, Arg29/F, and Arg90/F), and the fifth residue (Arg47/E) belongs to the E subunit. Residues Gln165, Arg167, and Arg222 play key roles in the binding of the pyrimidine moiety of the ligand (uridine, thymidine, uracil, and thymine) to VchUPh. Residues Glu197 and Thr93, as well as His7 of the adjacent subunit, play the main role in the binding of the furanose moiety of thymidine and uridine. The uridine (URI) molecule occupies the whole nucleoside-binding site of the VchUPh molecule. The URI molecule interacts with the nucleoside-binding site in the structure of VchUPh complexed with uridine (ID PDB: 5C80) through hydrogen bonds	Vibrio cholerae