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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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2
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Bezdekova J, Vodova M, Dolezelikova K, Zitka J, Smerkova K, Zitka O, Adam V, Vaculovicova M. Detection of microbial contamination based on uracil-selective synthetic receptors. Talanta 2021; 224:121813. [PMID: 33379038 DOI: 10.1016/j.talanta.2020.121813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/22/2022]
Abstract
The here presented work is focused on the development of a method for detection of microbial contamination of food based on uracil-selective synthetic receptors. Because uracil may serve as an indicator of bacterial contamination, its selective and on-site detection may prevent spreading of foodborne diseases. The synthetic receptors were created by molecular imprinting. Molecularly imprinted polymers for selective uracil isolation were prepared by a non-covalent imprinting method using dopamine as a functional monomer. Detection of isolated uracil was performed by capillary electrophoresis with absorption detection (λ - 260 nm). The conditions of preparation of molecularly imprinted polymers, their binding properties, adsorption kinetics and selectivity were investigated in detail. Furthermore, the prepared polymer materials were used for selective isolation and detection of uracil from complex samples as tomato products by miniaturized electrophoretic system suggesting the potential of in situ analysis of real samples.
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Affiliation(s)
- Jaroslava Bezdekova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Milada Vodova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
| | - Kristyna Dolezelikova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Jan Zitka
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Kristyna Smerkova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic
| | - Marketa Vaculovicova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00, Brno, Czech Republic.
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3
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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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4
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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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Abstract
We review literature on the metabolism of ribo- and deoxyribonucleotides, nucleosides, and nucleobases in Escherichia coli and Salmonella,including biosynthesis, degradation, interconversion, and transport. Emphasis is placed on enzymology and regulation of the pathways, at both the level of gene expression and the control of enzyme activity. The paper begins with an overview of the reactions that form and break the N-glycosyl bond, which binds the nucleobase to the ribosyl moiety in nucleotides and nucleosides, and the enzymes involved in the interconversion of the different phosphorylated states of the nucleotides. Next, the de novo pathways for purine and pyrimidine nucleotide biosynthesis are discussed in detail.Finally, the conversion of nucleosides and nucleobases to nucleotides, i.e.,the salvage reactions, are described. The formation of deoxyribonucleotides is discussed, with emphasis on ribonucleotidereductase and pathways involved in fomation of dUMP. At the end, we discuss transport systems for nucleosides and nucleobases and also pathways for breakdown of the nucleobases.
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6
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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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7
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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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9
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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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10
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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: 20] [Impact Index Per Article: 1.5] [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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11
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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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12
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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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13
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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: 15] [Impact Index Per Article: 1.1] [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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Paul D, O'Leary SE, Rajashankar K, Bu W, Toms A, Settembre EC, Sanders JM, Begley TP, Ealick SE. Glycal formation in crystals of uridine phosphorylase. Biochemistry 2010; 49:3499-509. [PMID: 20364833 PMCID: PMC2857653 DOI: 10.1021/bi902073b] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Uridine phosphorylase is a key enzyme in the pyrimidine salvage pathway. This enzyme catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate (or 2'-deoxyuridine to 2'-deoxyribose 1-phosphate). Here we report the structure of hexameric Escherichia coli uridine phosphorylase treated with 5-fluorouridine and sulfate and dimeric bovine uridine phosphorylase treated with 5-fluoro-2'-deoxyuridine or uridine, plus sulfate. In each case the electron density shows three separate species corresponding to the pyrimidine base, sulfate, and a ribosyl species, which can be modeled as a glycal. In the structures of the glycal complexes, the fluorouracil O2 atom is appropriately positioned to act as the base required for glycal formation via deprotonation at C2'. Crystals of bovine uridine phosphorylase treated with 2'-deoxyuridine and sulfate show intact nucleoside. NMR time course studies demonstrate that uridine phosphorylase can catalyze the hydrolysis of the fluorinated nucleosides in the absence of phosphate or sulfate, without the release of intermediates or enzyme inactivation. These results add a previously unencountered mechanistic motif to the body of information on glycal formation by enzymes catalyzing the cleavage of glycosyl bonds.
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Affiliation(s)
- Debamita Paul
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
| | - Seán E. O'Leary
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA
| | - Kanagalaghatta Rajashankar
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
- NE-CAT, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Weiming Bu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
| | - Angela Toms
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
| | - Ethan C. Settembre
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
| | - Jennie M. Sanders
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA
| | - Steven E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
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15
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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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16
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Lashkov AA, Zhukhlistova NE, Gabdulkhakov AG, Mikhailov AM. Comparative analysis of three-dimensional structures of homodimers of uridine phosphorylase from Salmonella typhimurium in the unligated state and in a complex with potassium ion. CRYSTALLOGR REP+ 2009. [DOI: 10.1134/s1063774509020151] [Citation(s) in RCA: 7] [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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17
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Roosild TP, Castronovo S, Fabbiani M, Pizzorno G. Implications of the structure of human uridine phosphorylase 1 on the development of novel inhibitors for improving the therapeutic window of fluoropyrimidine chemotherapy. BMC STRUCTURAL BIOLOGY 2009; 9:14. [PMID: 19291308 PMCID: PMC2664818 DOI: 10.1186/1472-6807-9-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Accepted: 03/16/2009] [Indexed: 11/10/2022]
Abstract
Background Uridine phosphorylase (UPP) is a key enzyme of pyrimidine salvage pathways, catalyzing the reversible phosphorolysis of ribosides of uracil to nucleobases and ribose 1-phosphate. It is also a critical enzyme in the activation of pyrimidine-based chemotherapeutic compounds such a 5-fluorouracil (5-FU) and its prodrug capecitabine. Additionally, an elevated level of this enzyme in certain tumours is believed to contribute to the selectivity of such drugs. However, the clinical effectiveness of these fluoropyrimidine antimetabolites is hampered by their toxicity to normal tissue. In response to this limitation, specific inhibitors of UPP, such as 5-benzylacyclouridine (BAU), have been developed and investigated for their ability to modulate the cytotoxic side effects of 5-FU and its derivatives, so as to increase the therapeutic index of these agents. Results In this report we present the high resolution structures of human uridine phosphorylase 1 (hUPP1) in ligand-free and BAU-inhibited conformations. The structures confirm the unexpected solution observation that the human enzyme is dimeric in contrast to the hexameric assembly present in microbial UPPs. They also reveal in detail the mechanism by which BAU engages the active site of the protein and subsequently disables the enzyme by locking the protein in a closed conformation. The observed inter-domain motion of the dimeric human enzyme is much greater than that seen in previous UPP structures and may result from the simpler oligomeric organization. Conclusion The structural details underlying hUPP1's active site and additional surfaces beyond these catalytic residues, which coordinate binding of BAU and other acyclouridine analogues, suggest avenues for future design of more potent inhibitors of this enzyme. Notably, the loop forming the back wall of the substrate binding pocket is conformationally different and substantially less flexible in hUPP1 than in previously studied microbial homologues. These distinctions can be utilized to discover novel inhibitory compounds specifically optimized for efficacy against the human enzyme as a step toward the development of more effective chemotherapeutic regimens that can selectively protect normal tissues with inherently lower UPP activity.
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Affiliation(s)
- Tarmo P Roosild
- Department of Drug Development, Nevada Cancer Institute, Las Vegas, Nevada, USA.
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Timofeev VI, Pavlyuk BF, Lashkov AA, Seregina TA, Gabdulkhakov AG, Vaĭnshteĭn BK, Mikhaĭlov AM. Structure of the homodimer of uridine phosphorylase from Salmonella typhimurium in the native state at 1.9 Å resolution. CRYSTALLOGR REP+ 2007. [DOI: 10.1134/s1063774507060235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Timofeev VI, Lashkov AA, Gabdoulkhakov AG, Pavlyuk BP, Kachalova GS, Betzel C, Morgunova EY, Zhukhlistova NE, Mikhailov AM. Isolation, crystallization and preliminary crystallographic analysis of Salmonella typhimurium uridine phosphorylase crystallized with 2,2'-anhydrouridine. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:852-4. [PMID: 17909287 PMCID: PMC2339722 DOI: 10.1107/s1744309107040560] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Accepted: 08/22/2007] [Indexed: 11/10/2022]
Abstract
Uridine phosphorylase (UPh; EC 2.4.2.3) is a member of the pyrimidine nucleoside phosphorylase family of enzymes which catalyzes the phosphorolytic cleavage of the C-N glycoside bond of uridine, with the formation of ribose 1-phosphate and uracil. This enzyme has been shown to be important in the activation and catabolism of fluoropyrimidines. Modulation of its enzymatic activity may affect the therapeutic efficacy of chemotherapeutic agents. The structural investigation of the bacterial uridine phosphorylases, both unliganded and complexed with substrate/product analogues and inhibitors, may help in understanding the catalytic mechanism of the phosphorolytic cleavage of uridine. Salmonella typhimurium uridine phosphorylase has been crystallized with 2,2'-anhydrouridine. X-ray diffraction data were collected to 2.15 A. Preliminary analysis of the diffraction data indicates that the crystal belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 88.52, b = 123.98, c = 133.52 A. The solvent content is 45.51%, assuming the presence of one hexamer molecule per asymmetric unit.
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Affiliation(s)
- Vladimir I. Timofeev
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninskiy Prospect 59, 119333 Moscow, Russia
| | - Alexander A. Lashkov
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninskiy Prospect 59, 119333 Moscow, Russia
| | - Azat G. Gabdoulkhakov
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninskiy Prospect 59, 119333 Moscow, Russia
| | - Bogdan Ph. Pavlyuk
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninskiy Prospect 59, 119333 Moscow, Russia
| | - Galina S. Kachalova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya Street 3, 142290 Pushchino, Moscow Region, Russia
| | - Christian Betzel
- Institute fur Biochemie und Lebensmittelchemie, University of Hamburg, c/o DESY, Building 22, Notkestrasse 85, 22604 Hamburg, Germany
| | - Ekaterina Yu. Morgunova
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninskiy Prospect 59, 119333 Moscow, Russia
| | - Nadezhda E. Zhukhlistova
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninskiy Prospect 59, 119333 Moscow, Russia
| | - Al’bert M. Mikhailov
- A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninskiy Prospect 59, 119333 Moscow, Russia
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