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Eistrikh-Heller PA, Rubinsky SV, Prokofev II, Gabdulkhakov AG, Mironov AS, Lashkov AA. X-Ray Structure and Molecular Dynamics Study of Uridine Phosphorylase from Vibrio cholerae in Complex with 2,2'-Anhydrouridine. CRYSTALLOGR REP+ 2020. [DOI: 10.1134/s1063774520020066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lashkov AA, Sotnichenko SE, Mikhailov AM. In silico analysis of the three-dimensional structures of the homodimer of uridine phosphorylase from Yersinia Pseudotuberculosis in the ligand-free state and in a complex with 5-fluorouracil. CRYSTALLOGR REP+ 2013. [DOI: 10.1134/s1063774513020156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lashkov AA, Gabdulkhakov AG, Prokofev II, Seregina TA, Sotnichenko SE, Lyashenko AV, Shtil AA, Mironov AS, Betzel C, Mikhailov AM. Expression, purification, crystallization and preliminary X-ray structure analysis of Vibrio cholerae uridine phosphorylase in complex with thymidine. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1394-7. [PMID: 23143257 PMCID: PMC3515389 DOI: 10.1107/s1744309112041401] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 10/02/2012] [Indexed: 11/10/2022]
Abstract
A high-resolution structure of the complex of Vibrio cholerae uridine phosphorylase (VchUPh) with its physiological ligand thymidine is important in order to determine the mechanism of the substrate specificity of the enzyme and for the rational design of pharmacological modulators. Here, the expression and purification of VchUPh and the crystallization of its complex with thymidine are reported. Conditions for crystallization were determined with an automated Cartesian Dispensing System using The Classics, MbClass and MbClass II Suites crystallization kits. Crystals of the VchUPh-thymidine complex (of dimensions ∼200-350 µm) were grown by the sitting-drop vapour-diffusion method in ∼7 d at 291 K. The crystallization solution consisted of 1.5 µl VchUPh (15 mg ml(-1)), 1 µl 0.1 M thymidine and 1.5 µl reservoir solution [15%(w/v) PEG 4000, 0.2 M MgCl(2).6H2O in 0.1 M Tris-HCl pH 8.5]. The crystals diffracted to 2.12 Å resolution and belonged to space group P2(1) (No. 4), with unit-cell parameters a=91.80, b=95.91, c=91.89 Å, β=119.96°. The Matthews coefficient was calculated as 2.18 Å3 Da(-1); the corresponding solvent content was 43.74%.
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Affiliation(s)
- Alexander A. Lashkov
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - Azat G. Gabdulkhakov
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - Igor I. Prokofev
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - Tatyana A. Seregina
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 119333, Russian Federation
- State Research Institute of Genetics and Selection of Industrial Microorganisms, 1st Dorozhny Proezd 1, Moscow 117545, Russian Federation
| | - Sergey E. Sotnichenko
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - Andrey V. Lyashenko
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - Alexander A. Shtil
- Blokhin Cancer Center, Kashirskoye Shosse 24, Moscow 115478, Russian Federation
| | - Alexander S. Mironov
- State Research Institute of Genetics and Selection of Industrial Microorganisms, 1st Dorozhny Proezd 1, Moscow 117545, Russian Federation
| | | | - Al’bert M. Mikhailov
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 119333, Russian Federation
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Lashkov AA, Zhukhlistova NE, Sotnichenko SE, Gabdulkhakov AG, Mikhailov AM. Structural basis for the mechanism of inhibition of uridine phosphorylase from Salmonella typhimurium. CRYSTALLOGR REP+ 2010. [DOI: 10.1134/s1063774510010098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lashkov AA, Zhukhlistova NE, Gabdoulkhakov AH, Shtil AA, Efremov RG, Betzel C, Mikhailov AM. The X-ray structure of Salmonella typhimurium uridine nucleoside phosphorylase complexed with 2,2'-anhydrouridine, phosphate and potassium ions at 1.86 A resolution. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 66:51-60. [PMID: 20057049 DOI: 10.1107/s0907444909044175] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 10/23/2009] [Indexed: 11/10/2022]
Abstract
Uridine nucleoside phosphorylase is an important drug target for the development of anti-infective and antitumour agents. The X-ray crystal structure of Salmonella typhimurium uridine nucleoside phosphorylase (StUPh) complexed with its inhibitor 2,2'-anhydrouridine, phosphate and potassium ions has been solved and refined at 1.86 A resolution (R(cryst) = 17.6%, R(free) = 20.6%). The complex of human uridine phosphorylase I (HUPhI) with 2,2'-anhydrouridine was modelled using a computational approach. The model allowed the identification of atomic groups in 2,2'-anhydrouridine that might improve the interaction of future inhibitors with StUPh and HUPhI.
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Affiliation(s)
- Alexander A Lashkov
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, 59 Leninsky Prospect, 119333 Moscow, Russia
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