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Antipov A, Okorokova N, Mordkovich N, Safonova T, Veiko V. Role of phosphate-coordinating arginine residues in the thermal stability of uridine phosphorylase from Shewanella oneidensis MR-1. Biochimie 2024; 225:19-25. [PMID: 38723939 DOI: 10.1016/j.biochi.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/15/2024] [Accepted: 05/06/2024] [Indexed: 05/24/2024]
Abstract
The role of phosphate-coordinating arginine residues in the thermal stability of uridine phosphorylase from Shewanella oneidensis MR-1 was investigated by mutation analysis. Uridine phosphorylase mutant genes were constructed by site-directed mutagenesis. The enzyme mutants were prepared and isolated, and their kinetic parameters were determined. It was shown that all these arginine residues play an important role both in the catalysis and thermal stability. The arginine residues 176 were demonstrated to form a kind of a phosphate pore in the hexameric structure of uridine phosphorylase, and they not only contribute to thermal stabilization of the enzyme but also have a regulatory function. The replacement of arginine 176 with an alanine residue resulted in a significant decrease in the kinetic stability of the enzyme but led to a twofold increase in its specific activity.
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Affiliation(s)
- Alexey Antipov
- A.N. Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Science, Moscow, Russia.
| | - Natalya Okorokova
- A.N. Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Science, Moscow, Russia
| | - Nadezhda Mordkovich
- A.N. Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Science, Moscow, Russia
| | - Tatyana Safonova
- A.N. Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Science, Moscow, Russia
| | - Vladimir Veiko
- A.N. Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Science, Moscow, Russia
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Eistrikh-Heller PA, Rubinsky SV, Samygina VR, Gabdulkhakov AG, Kovalchuk MV, Mironov AS, Lashkov AA. Crystallization in Microgravity and the Atomic-Resolution Structure of Uridine Phosphorylase from Vibrio cholerae. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Uridine phosphorylases are known as key targets for the development of new anticancer and antiparasitic agents. Crystals of uridine phosphorylase from the pathogenic bacterium Vibrio cholerae were grown in microgravity by the capillary counter-diffusion method on board of the International Space Station. The three-dimensional structure of this enzyme was determined at atomic (1.04 Å) resolution (RCSB PDB ID: 6Z9Z). Alternative conformations of long fragments (β-strands and adjacent loops) of the protein molecule were found for the first time in the three-dimensional structure of uridine phosphorylase in the absence of specific bound ligands. Apparently, these alternative conformations are related to the enzyme function. Conformational analysis with Markov state models demonstrated that conformational rearrangements can occur in the ligand-free state of the enzyme.
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Strained Conformations of Nucleosides in Active Sites of Nucleoside Phosphorylases. Biomolecules 2020; 10:biom10040552. [PMID: 32260512 PMCID: PMC7226091 DOI: 10.3390/biom10040552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/26/2020] [Accepted: 04/01/2020] [Indexed: 11/28/2022] Open
Abstract
Nucleoside phosphorylases catalyze the reversible phosphorolysis of nucleosides to heterocyclic bases, giving α-d-ribose-1-phosphate or α-d-2-deoxyribose-1-phosphate. These enzymes are involved in salvage pathways of nucleoside biosynthesis. The level of these enzymes is often elevated in tumors, which can be used as a marker for cancer diagnosis. This review presents the analysis of conformations of nucleosides and their analogues in complexes with nucleoside phosphorylases of the first (NP-1) family, which includes hexameric and trimeric purine nucleoside phosphorylases (EC 2.4.2.1), hexameric and trimeric 5′-deoxy-5′-methylthioadenosine phosphorylases (EC 2.4.2.28), and uridine phosphorylases (EC 2.4.2.3). Nucleosides adopt similar conformations in complexes, with these conformations being significantly different from those of free nucleosides. In complexes, pentofuranose rings of all nucleosides are at the W region of the pseudorotation cycle that corresponds to the energy barrier to the N↔S interconversion. In most of the complexes, the orientation of the bases with respect to the ribose is in the high-syn region in the immediate vicinity of the barrier to syn ↔ anti transitions. Such conformations of nucleosides in complexes are unfavorable when compared to free nucleosides and they are stabilized by interactions with the enzyme. The sulfate (or phosphate) ion in the active site of the complexes influences the conformation of the furanose ring. The binding of nucleosides in strained conformations is a characteristic feature of the enzyme–substrate complex formation for this enzyme group.
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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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Prokofev II, Lashkov AA, Gabdulkhakov AG, Balaev VV, Mironov AS, Betzel C, Mikhailov AM. Structural and Functional Analysis of Pyrimidine Nucleoside Phosphorylases of the NP-I and NP-II Families in Complexes with 6-Methyluracil. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s1063774518030239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Mordkovich NN, Safonova TN, Antipov AN, Manuvera VA, Polyakov KM, Okorokova NA, Veiko VP. Study of Structural-Functional Organization of Nucleoside Phosphorylases of Gammaproteobacteria. Special Aspects of Functioning of Uridine Phosphorylase Phosphate-Binding Site. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818010064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Decoding the similarities and differences among mycobacterial species. PLoS Negl Trop Dis 2017; 11:e0005883. [PMID: 28854187 PMCID: PMC5595346 DOI: 10.1371/journal.pntd.0005883] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 09/12/2017] [Accepted: 08/18/2017] [Indexed: 11/19/2022] Open
Abstract
Mycobacteriaceae comprises pathogenic species such as Mycobacterium tuberculosis, M. leprae and M. abscessus, as well as non-pathogenic species, for example, M. smegmatis and M. thermoresistibile. Genome comparison and annotation studies provide insights into genome evolutionary relatedness, identify unique and pathogenicity-related genes in each species, and explore new targets that could be used for developing new diagnostics and therapeutics. Here, we present a comparative analysis of ten-mycobacterial genomes with the objective of identifying similarities and differences between pathogenic and non-pathogenic species. We identified 1080 core orthologous clusters that were enriched in proteins involved in amino acid and purine/pyrimidine biosynthetic pathways, DNA-related processes (replication, transcription, recombination and repair), RNA-methylation and modification, and cell-wall polysaccharide biosynthetic pathways. For their pathogenicity and survival in the host cell, pathogenic species have gained specific sets of genes involved in repair and protection of their genomic DNA. M. leprae is of special interest owing to its smallest genome (1600 genes and ~1300 psuedogenes), yet poor genome annotation. More than 75% of the pseudogenes were found to have a functional ortholog in the other mycobacterial genomes and belong to protein families such as transferases, oxidoreductases and hydrolases. Members of the Mycobacteriaceae family, which are known to adapt to different environmental niches, comprise bacterial species with varied genome sizes. They are unique in their cell-wall composition, which is remarkably thick and lipid-rich as compared to other bacteria. We performed a comparative analysis at the proteome level for ten mycobacterial species that differ in their pathogenicity, genome size and environmental niches. A total of 1080 orthologous clusters with representation from all ten species were obtained, and these were further examined for their domain annotations, domain architecture similarities and enriched GO terms. These core orthologous clusters are enriched in various biosynthetic pathways. The proteins that are specific to each of the ten species were also investigated for their GO functions. The M. leprae genome has a large number of pseudogenes and we searched for their functional orthologs in other mycobacterial species in order to understand the functions that are lost from the M. leprae genome. The proteins present exclusively in M. leprae genome were studied in more detail, in order to predict putative drug targets and diagnostic markers. These findings, which have implications in understanding evolution of mycobacterial genomes, identify species-specific proteins that have potential for use in developing new diagnostic tools and therapeutics.
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Prokofev II, Lashkov AA, Gabdulkhakov AG, Balaev VV, Seregina TA, Mironov AS, Betzel C, Mikhailov AM. 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. CRYSTALLOGR REP+ 2016. [DOI: 10.1134/s1063774516060134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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9
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Lashkov AA, Shchekotikhin AA, Shtil AA, Sotnichenko SE, Mikhailov AM. Modified 5-fluorouracil: Uridine phosphorylase inhibitor. CRYSTALLOGR REP+ 2016. [DOI: 10.1134/s1063774516050138] [Citation(s) in RCA: 2] [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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10
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Safonova TN, Mordkovich NN, Veiko VP, Okorokova NA, Manuvera VA, Dorovatovskii PV, Popov VO, Polyakov KM. Concerted action of two subunits of the functional dimer of Shewanella oneidensis MR-1 uridine phosphorylase derived from a comparison of the C212S mutant and the wild-type enzyme. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:203-10. [PMID: 26894668 DOI: 10.1107/s2059798315024353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/17/2015] [Indexed: 11/10/2022]
Abstract
Uridine phosphorylase (UP; EC 2.4.2.3), a key enzyme in the pyrimidine-salvage pathway, catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. The structure of the C212S mutant of uridine phosphorylase from the facultatively aerobic Gram-negative γ-proteobacterium Shewanella oneidensis MR-1 (SoUP) was determined at 1.68 Å resolution. A comparison of the structures of the mutant and the wild-type enzyme showed that one dimer in the mutant hexamer differs from all other dimers in the mutant and wild-type SoUP (both in the free form and in complex with uridine). The key difference is the `maximum open' state of one of the subunits comprising this dimer, which has not been observed previously for uridine phosphorylases. Some conformational features of the SoUP dimer that provide access of the substrate into the active site are revealed. The binding of the substrate was shown to require the concerted action of two subunits of the dimer. The changes in the three-dimensional structure induced by the C212S mutation account for the lower affinity of the mutant for inorganic phosphate, while the affinity for uridine remains unchanged.
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Affiliation(s)
- T N Safonova
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
| | - N N Mordkovich
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
| | - V P Veiko
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
| | - N A Okorokova
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
| | - V A Manuvera
- Scientific Research Institute of Physical-Chemical Medicine, Federal Medical-Biological Agency, 1a Malaya Pirogovskaya St., Moscow 119435, Russian Federation
| | - P V Dorovatovskii
- National Research Centre `Kurchatov Institute', 1 Pl. Akademika Kurchatova, Moscow 123182, Russian Federation
| | - V O Popov
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
| | - K M Polyakov
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
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Balaev VV, Lashkov AA, Gabdulkhakov AG, Dontsova MV, Mironov AS, Betzel C, Mikhailov AM. Three-dimensional structures of unligated uridine phosphorylase from Yersinia pseudotuberculosis at 1.4 Å resolution and its complex with an antibacterial drug. CRYSTALLOGR REP+ 2015. [DOI: 10.1134/s1063774515040069] [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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12
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Safonova TN, Mikhailov SN, Veiko VP, Mordkovich NN, Manuvera VA, Alekseev CS, Kovalchuk MV, Popov VO, Polyakov KM. High-synconformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures ofShewanella oneidensisMR-1 uridine phosphorylase in the free form and in complex with uridine. ACTA ACUST UNITED AC 2014; 70:3310-9. [DOI: 10.1107/s1399004714024079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/31/2014] [Indexed: 11/10/2022]
Abstract
Uridine phosphorylase (UP; EC 2.4.2.3), a key enzyme in the pyrimidine-salvage pathway, catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. Expression of UP fromShewanella oneidensisMR-1 (SoUP) was performed inEscherichia coli. The high-resolution X-ray structure of SoUP was solved in the free form and in complex with uridine. A crystal of SoUP in the free form was grown under microgravity and diffracted to ultrahigh resolution. Both forms of SoUP contained sulfate instead of phosphate in the active site owing to the presence of ammonium sulfate in the crystallization solution. The latter can be considered as a good mimic of phosphate. In the complex, uridine adopts a high-synconformation with a nearly planar ribose ring and is present only in one subunit of the hexamer. A comparison of the structures of SoUP in the free form and in complex with the natural substrate uridine showed that the subunits of the hexamer are not identical, with the active sites having either an open or a closed conformation. In the monomers with the closed conformation, the active sites in which uridine is absent contain a glycerol molecule mimicking the ribose moiety of uridine.
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Prokofev II, Lashkov AA, Gabdulkhakov AG, Dontsova MV, Seregina TA, Mironov AS, Betzel C, Mikhailov AM. Crystallization and preliminary X-ray study of Vibrio cholerae uridine phosphorylase in complex with 6-methyluracil. Acta Crystallogr F Struct Biol Commun 2014; 70:60-3. [PMID: 24419619 PMCID: PMC3943090 DOI: 10.1107/s2053230x13031877] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 11/22/2013] [Indexed: 11/10/2022] Open
Abstract
Uridine phosphorylase catalyzes the phosphorolysis of ribonucleosides, with the nitrogenous base and ribose 1-phosphate as products. Additionally, it catalyzes the reverse reaction of the synthesis of ribonucleosides from ribose 1-phosphate and a nitrogenous base. However, the enzyme does not catalyze the synthesis of nucleosides when the substrate is a nitrogenous base substituted at the 6-position, such as 6-methyluracil (6-MU). In order to explain this fact, it is essential to investigate the three-dimensional structure of the complex of 6-MU with uridine phosphorylase. 6-MU is a pharmaceutical agent that improves tissue nutrition and enhances cell regeneration by normalization of nucleotide exchange in humans. 6-MU is used for the treatment of diseases of the gastrointestinal tract, including infectious diseases. Here, procedures to obtain the uridine phosphorylase from the pathogenic bacterium Vibrio cholerae (VchUPh), purification of this enzyme, crystallization of the complex of VchUPh with 6-MU, and X-ray data collection and preliminary X-ray analysis of the VchUPh-6-MU complex at atomic resolution are reported.
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Affiliation(s)
- Igor I. Prokofev
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 117333, Russian Federation
| | - Alexander A. Lashkov
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 117333, Russian Federation
| | - Azat G. Gabdulkhakov
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 117333, Russian Federation
| | - Mariya V. Dontsova
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 117333, Russian Federation
| | - Tatyana A. Seregina
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow 117333, 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 117333, Russian Federation
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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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15
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Lashkov AA, Sotnichenko SE, Prokofiev II, Gabdulkhakov AG, Agapov II, Shtil AA, Betzel C, Mironov AS, Mikhailov AM. X-ray structure of Salmonella typhimurium uridine phosphorylase complexed with 5-fluorouracil and molecular modelling of the complex of 5-fluorouracil with uridine phosphorylase from Vibrio cholerae. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:968-74. [PMID: 22868762 DOI: 10.1107/s090744491201815x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 04/23/2012] [Indexed: 11/10/2022]
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.
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Affiliation(s)
- Alexander A Lashkov
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, 59 Leninsky Prospekt, 119333 Moscow, Russian Federation
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16
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Roosild TP, Castronovo S, Villoso A, Ziemba A, Pizzorno G. A novel structural mechanism for redox regulation of uridine phosphorylase 2 activity. J Struct Biol 2011; 176:229-37. [PMID: 21855639 DOI: 10.1016/j.jsb.2011.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 08/02/2011] [Accepted: 08/02/2011] [Indexed: 01/16/2023]
Abstract
Uridine phosphorylase (UPP) catalyzes the reversible conversion of uridine to uracil and ribose-1-phosphate and plays an important pharmacological role in activating fluoropyrimidine nucleoside chemotherapeutic agents such as 5-fluorouracil and capecitabine. Most vertebrate animals, including humans, possess two homologs of this enzyme (UPP1 & UPP2), of which UPP1 has been more thoroughly studied and is better characterized. Here, we report two crystallographic structures of human UPP2 (hUPP2) in distinctly active and inactive conformations. These structures reveal that a conditional intramolecular disulfide bridge can form within the protein that dislocates a critical phosphate-coordinating arginine residue (R100) away from the active site, disabling the enzyme. In vitro activity measurements on both recombinant hUPP2 and native mouse UPP2 confirm the redox sensitivity of this enzyme, in contrast to UPP1. Sequence analysis shows that this feature is conserved among UPP2 homologs and lacking in all UPP1 proteins due to the absence of a necessary cysteine residue. The state of the disulfide bridge has further structural consequences for one face of the enzyme that suggest UPP2 may have additional functions in sensing and initiating cellular responses to oxidative stress. The molecular details surrounding these dynamic aspects of hUPP2 structure and regulation provide new insights as to how novel inhibitors of this protein may be developed with improved specificity and affinity. As uridine is emerging as a promising protective compound in neuro-degenerative diseases, including Alzheimer's and Parkinson's, understanding the regulatory mechanisms underlying UPP control of uridine concentration is key to improving clinical outcomes in these illnesses.
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Affiliation(s)
- Tarmo P Roosild
- Department of Drug Development, Nevada Cancer Institute, One Breakthrough Way, Las Vegas, NV 89135, USA.
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Lashkov AA, Zhukhlistova NE, Seregina TA, Gabdulkhakov AG, Mikhailov AM. Uridine phosphorylase in biomedical, structural, and functional aspects: A review. CRYSTALLOGR REP+ 2011. [DOI: 10.1134/s1063774511040122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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18
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Tran TH, Christoffersen S, Allan PW, Parker WB, Piskur J, Serra I, Terreni M, Ealick SE. The crystal structure of Streptococcus pyogenes uridine phosphorylase reveals a distinct subfamily of nucleoside phosphorylases. Biochemistry 2011; 50:6549-58. [PMID: 21707079 DOI: 10.1021/bi200707z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Uridine phosphorylase (UP), a key enzyme in the pyrimidine salvage pathway, catalyzes the reversible phosphorolysis of uridine or 2'-deoxyuridine to uracil and ribose 1-phosphate or 2'-deoxyribose 1-phosphate. This enzyme belongs to the nucleoside phosphorylase I superfamily whose members show diverse specificity for nucleoside substrates. Phylogenetic analysis shows Streptococcus pyogenes uridine phosphorylase (SpUP) is found in a distinct branch of the pyrimidine subfamily of nucleoside phosphorylases. To further characterize SpUP, we determined the crystal structure in complex with the products, ribose 1-phosphate and uracil, at 1.8 Å resolution. Like Escherichia coli UP (EcUP), the biological unit of SpUP is a hexamer with an α/β monomeric fold. A novel feature of the active site is the presence of His169, which structurally aligns with Arg168 of the EcUP structure. A second active site residue, Lys162, is not present in previously determined UP structures and interacts with O2 of uracil. Biochemical studies of wild-type SpUP showed that its substrate specificity is similar to that of EcUP, while EcUP is ∼7-fold more efficient than SpUP. Biochemical studies of SpUP mutants showed that mutations of His169 reduced activity, while mutation of Lys162 abolished all activity, suggesting that the negative charge in the transition state resides mostly on uracil O2. This is in contrast to EcUP for which transition state stabilization occurs mostly at O4.
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Affiliation(s)
- Timothy H Tran
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
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Roosild TP, Castronovo S. Active site conformational dynamics in human uridine phosphorylase 1. PLoS One 2010; 5:e12741. [PMID: 20856879 PMCID: PMC2939078 DOI: 10.1371/journal.pone.0012741] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 08/20/2010] [Indexed: 11/18/2022] Open
Abstract
Uridine phosphorylase (UPP) is a central enzyme in the pyrimidine salvage pathway, catalyzing the reversible phosphorolysis of uridine to uracil and ribose-1-phosphate. Human UPP activity has been a focus of cancer research due to its role in activating fluoropyrimidine nucleoside chemotherapeutic agents such as 5-fluorouracil (5-FU) and capecitabine. Additionally, specific molecular inhibitors of this enzyme have been found to raise endogenous uridine concentrations, which can produce a cytoprotective effect on normal tissues exposed to these drugs. Here we report the structure of hUPP1 bound to 5-FU at 2.3 A resolution. Analysis of this structure reveals new insights as to the conformational motions the enzyme undergoes in the course of substrate binding and catalysis. The dimeric enzyme is capable of a large hinge motion between its two domains, facilitating ligand exchange and explaining observed cooperativity between the two active sites in binding phosphate-bearing substrates. Further, a loop toward the back end of the uracil binding pocket is shown to flexibly adjust to the varying chemistry of different compounds through an "induced-fit" association mechanism that was not observed in earlier hUPP1 structures. The details surrounding these dynamic aspects of hUPP1 structure and function provide unexplored avenues to develop novel inhibitors of this protein with improved specificity and increased affinity. Given the recent emergence of new roles for uridine as a neuron protective compound in ischemia and degenerative diseases, such as Alzheimer's and Parkinson's, inhibitors of hUPP1 with greater efficacy, which are able to boost cellular uridine levels without adverse side-effects, may have a wide range of therapeutic applications.
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Affiliation(s)
- Tarmo P Roosild
- Department of Drug Development, Nevada Cancer Institute, Las Vegas, Nevada, United States of America.
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