title: Structural investigation of the thymidine phosphorylase from Salmonella typhimurium in the unliganded state and its complexes with thymidine and uridine.
abstract: Highly specific thymidine phosphorylases catalyze the phosphorolytic cleavage of thymidine, with the help of a phosphate ion, resulting in thymine and 2-deoxy-α-D-ribose 1-phosphate. Thymidine phosphorylases do not catalyze the phosphorolysis of uridine, in contrast to nonspecific pyrimidine nucleoside phosphorylases and uridine phosphorylases. Understanding the mechanism of substrate specificity on the basis of the nucleoside is essential to support rational drug-discovery investigations of new antitumour and anti-infective drugs which are metabolized by thymidine phosphorylases. For this reason, X-ray structures of the thymidine phosphorylase from Salmonella typhimurium were solved and refined: the unliganded structure at 2.05 Å resolution (PDB entry 4xr5), the structure of the complex with thymidine at 2.55 Å resolution (PDB entry 4yek) and that of the complex with uridine at 2.43 Å resolution (PDB entry 4yyy). The various structural features of the enzyme which might be responsible for the specificity for thymidine and not for uridine were identified. The presence of the 2'-hydroxyl group in uridine results in a different position of the uridine furanose moiety compared with that of thymidine. This feature may be the key element of the substrate specificity. The specificity might also be associated with the opening/closure mechanism of the two-domain subunit structure of the enzyme.
authors.affiliation: A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation.
authors.forename: Vladislav V
authors.initials: VV
authors.lastname: Balaev
authors.affiliation: A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation.
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Lashkov
authors.affiliation: A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation.
authors.forename: Azat G
authors.initials: AG
authors.lastname: Gabdulkhakov
authors.affiliation: A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation.
authors.forename: Maria V
authors.initials: MV
authors.lastname: Dontsova
authors.affiliation: State Research Institute of Genetics and Selection of Industrial Microorganisms, 1-st Dorozhny Proezd 1, Moscow 117545, Russian Federation.
authors.forename: Tatiana A
authors.initials: TA
authors.lastname: Seregina
authors.affiliation: State Research Institute of Genetics and Selection of Industrial Microorganisms, 1-st Dorozhny Proezd 1, Moscow 117545, Russian Federation.
authors.forename: Alexander S
authors.initials: AS
authors.lastname: Mironov
authors.affiliation: Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Institute of Biochemistry and Molecular Biology, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Betzel
authors.affiliation: A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation.
authors.forename: Al'bert M
authors.initials: AM
authors.lastname: Mikhailov
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D020134:Catalytic Domain; D003460:Crystallization; D018360:Crystallography, X-Ray; D008024:Ligands; D011485:Protein Binding; D012486:Salmonella typhimurium / Q000201:enzymology*; D013379:Substrate Specificity; D013939:Thymidine Phosphorylase / Q000737:chemistry*; D013942:Thymine Nucleotides / Q000737:chemistry*; D014529:Uridine / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D008024:Ligands; D013942:Thymine Nucleotides; D013939:Thymidine Phosphorylase; D014529:Uridine
keywords: Salmonella typhimurium; X-ray analysis; nucleoside phosphorylases; nucleosides; protein crystallography; substrate specificity; thymidine phosphorylase