Substrate specificity of E. coli uridine phosphorylase. Further evidences of high-syn conformation of the substrate in uridine phosphorolysis

References

• Pugmire, M.; Ealick, S. Structural analyses reveal two distinct families of nucleoside phosphorylases. Biochem. J. 2002, 361, 1–25.
   PubMed Web of Science ®Google Scholar
• Lewkowicz, E.S.; Iribarren, A.M. Nucleoside Phosphorylases. Curr. Org. Chem. 2006, 10, 1197–1215.
   Web of Science ®Google Scholar
• Yan, R.; Wan, L.; Pizzorno, G.; Cao, D. Uridine phosphorylase in breast cancer: a new prognostic factor. Front Biosci. 2006, 11, 2759–2766.
   PubMed Web of Science ®Google Scholar
• Utagawa, T. Enzymatic preparation of nucleoside antibiotics. J. Mol. Catal. B: Enzym. 1999, 6, 215–222.
   Web of Science ®Google Scholar
• Zaks, A. Industrial biocatalysis. Curr. Opin. Chem. Biol. 2001, 5, 130–136
   PubMed Web of Science ®Google Scholar
• Mikhailopulo, I.A. Biotechnology of nucleic acid constituents-State of the art and perspectives. Curr. Org. Chem. 2007, 11, 317–335.
   Web of Science ®Google Scholar
• Iglesias, L.E.; Lewkowicz, E.S.; Medici, R.; Bianchi, P.; Iribarren, A.M. Biocatalytic approaches applied to the synthesis of nucleoside prodrugs. Biotechnol. Adv. 2015, 33, 412–434.
   PubMed Web of Science ®Google Scholar
• Konstantinova, I.D.; Antonov, K.V.; Fateev, I.V.; Miroshnikov, A.I.; Stepchenko, V.A.; Baranovsky, A.V.; Mikhailopulo, I.A. A Chemo-Enzymatic Synthesis of β;-D-Arabinofuranosyl Purine Nucleosides. Synthesis 2011, 1555–1560.
   Web of Science ®Google Scholar
• Kulikowska, E.; Bzowska, A.; Wierzchowski, J.; Shugar, D. Properties of two unusual, and fluorescent, substrates of purine-nucleoside phosphorylase: 7-methylguanosine and 7-methylinosine. Biochimica et Biophys. Acta (BBA)-Protein Struct. Mol. Enzymology. 1986, 874, 355–363.
   PubMed Web of Science ®Google Scholar
• Hennen, W.J.; Wong, C.H. A new method for the enzymic synthesis of nucleosides using purine nucleoside phosphorylase. J. Org. Chem. 1989, 54 (19), 4692–4695.
   Web of Science ®Google Scholar
• Nixon, A.E.; Hunter, J.L.; Bonifacio, G.; Eccleston, J.F.; Webb, M.R. Purine nucleoside phosphorylase: its use in a spectroscopic assay for inorganic phosphate and for removing inorganic phosphate with the aid of phosphodeoxyribomutase. Anal. Biochem. 1998, 265, 299–307.
   PubMed Web of Science ®Google Scholar
• Ubiali, D.; Morelli, C.F.; Rabuffetti, M.; Cattaneo, G.; Serra, I.; Bavaro, T.; Speranza, G. Substrate Specificity of a Purine Nucleoside Phosphorylase from Aeromonas hydrophila Toward 6-Substituted Purines and its Use as a Biocatalyst in the Synthesis of the Corresponding Ribonucleosides. Curr. Org. Chem. 2015, 19, 2220–2225.
   Web of Science ®Google Scholar
• Krenitsky, T.A. Uridine phosphorylase from Escherichia coli: Kinetic properties and mechanism. Biochimica et Biophys. Acta (BBA)-Enzymology 1976, 429 (2), 352–358.
   PubMed Web of Science ®Google Scholar
• Leer, J.C.; Hammer-Jespersen, K.; Schwartz, M. Uridine Phosphorylase from Escherichia coli. Physical and Chemical Characterization. Eur. J. Biochem. 1977, 75, 217–224.
   PubMedGoogle Scholar
• Niedzwicki, J.G.; El Kouni, M.H.; Chu, S.H.; Cha, S. Structure-activity relationship of ligands of the pyrimidine nucleoside phosphorylases. Biochem. Pharmacol. 1983, 32, 399–415.
   PubMed Web of Science ®Google Scholar
• el Kouni, M.H.; Naguib, F.N.; Chu, S.H.; Cha, S.M.; Ueda, T.; Gosselin, G.; Imbach, J.-L.; Sheally, F.; Otter, B.A. Effect of the N-glycosidic bond conformation and modifications in the pentose moiety on the binding of nucleoside ligands to uridine phosphorylase. Mol. Pharmacol. 1988, 34, 104–110.
   PubMed Web of Science ®Google Scholar
• el Kouni, M.H.; Naguib, F.N.; Panzica, R.P.; Otter, B.A.; Chu, S.H.; Gosselin, G.; Chu, C.K.; Schinazi, R.F.; Shealy, Y.F.; Goudgaon, N.; Ozerov, A.A.; Ueda, T.; Iltzsch, M.H. Effects of modifications in the pentose moiety and conformational changes on the binding of nucleoside ligands to uridine phosphorylase fromToxoplasma gondii. Biochem. Pharmacol. 1996, 51, 1687–1700.
   PubMed Web of Science ®Google Scholar
• Krajewska, E.; Shugar, D. Pyrimidine ribonucleoside phosphorylase activity vs 5-and/or 6-substituted uracil and uridine analogues, including conformational aspects. Biochem. Pharmacol. 1982, 31(6), 1097–1102.
   PubMed Web of Science ®Google Scholar
• GordonA.J.; FordR.A. In: The Chemist's Companion: A Handbook of Practical Data, Techniques, and References. 1973, New-York: Wiley-Interscience.
   Google Scholar
• Panova, N.G.; Alexeev, C.S.; Kuzmichov, A.S.; Shcheveleva, E.V.; Gavryushov, S.A.; Polyakov, K.M.; Kritzyn, A.M.; Mikhailov, S.N.; Esipov, R.S.; Miroshnikov, A.I. Substrate specificity of E. coli thymidine phosphorylase. Biochemistry (Moscow) 2007, 72(1), 21–28.
   PubMed Web of Science ®Google Scholar
• Alexeev, C.S.; Polyakov, K.M.; Sivets, G.G.; Safonova, T.N.; Mikhailov, S.N. Substrate specificity of E. coli uridine phosphorylase. Evidence of high-syn conformation of substrate. Collect. Symp. Ser. 2014, 14, 213–216.
   Google Scholar
• Wagner, G.; Jochims, J.C. Barrieren der behinderten Rotation urn die N-glycosidische Bindung. IV. 1-(β;-D-Ribofuranosy1)isocyanursauren. Chem. Ber. 1979, 112, 1941–1947.
   Google Scholar
• Thibaudeau, C.; Acharya, P.; Chattopadhyaya, J. In: Stereoelectronic effects in nucleosides and nucleotides and their structural implications. 2005, Sweden: Uppsala University Press.
   Google Scholar
• Moiseyev, G.P.; Yakovlev, G.I.; Lysov, Yu.P.; Chernyi, A.A.; Polyakov, K.M.; Oivanen, M.; Lonnberg, H.; Beigelman, L.N.; Efimtseva, E.V.; Mikhailov, S.N. Determination of the nucleotide conformation in the productive enzyme-substrate complexes of RNA-depolymerases. FEBS Lett. 1997, 404, 169–172.
   PubMed Web of Science ®Google Scholar
• Tunitskaya, V.L.; Rusakova, E.E.; Padyukova, N.Sh.; Ermolinsky, B.S.; Chernyi, A.A.; Kochetkov, S.N.; Lysov, Yu.P.; Mikhailov, S.N. Substrate properties of C'-methyl UTP derivatives in T7 RNA polymerase reactions. Evidence for N-type NTP conformation. FEBS Lett. 1997, 400, 263–266.
   PubMed Web of Science ®Google Scholar
• Mikhailov, S.N.; Lysov, Yu.P.; YakovlevG.I. Use of functionally competent nucleosides and nucleotide analogs in studying enzyme-substrate interactions (review). Mol. Biol. (Russia) 1999, 33, 340–354.
   Web of Science ®Google Scholar
• Safonova, T.N.; Mikhailov, S.N.; Veiko, V.P.; Mordkovich, N.N.; Manuvera, V.A.; Alekseev, C.S.; Kovalchuk, M.V.; Popov, V.O.; PolyakovK.M. High-syn conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis MR-1 uridine phosphorylase in the free form and in complex with uridine. Acta Crystallogr. D. 2014, D70, 3310–3319.
   Google Scholar
• Mordkovich, N.N.; Safonova, T.N.; Manuvera, V.A.; Veiko, V.P.; Polyakov, K.M.; Alekseev, K.S.; Mikhailov, S.N.; PopovV.O. Physicochemical Characterization of Uridine Phosphorylase from Shewanella oneidensis MR-1. Dokl. Biochem. Biophys. (Russia) 2013, 451, 187–189.
   PubMed Web of Science ®Google Scholar
• Panova, N.G.; Shcheveleva, E.V.; Alexeev, C.S.; Mukhortov, V.G.; Zuev, A.N.; Mikhailov, S.N.; Esipov, R.S.; Chuvikovsky, D.V.; Miroshnikov, A.I. Using of 4-thiouridine and 4-thiothymidine for pyrimidine nucleoside phosphorylase studying. Mol. Biol. (Russia) 2004, 38, 770–776.
   Web of Science ®Google Scholar
• Mikhailov, S.N.; Padyukova, N.S.; Karpeiskii, M.Y.; Kolobushkina, L.I.; Beigelman, L.N. (). Use of 5-deoxy-ribo-hexofuranose derivatives for the preparation of 5′-nucleotide phosphonates and homoribonucleosides. Collect. Czech. Chem. Commun. 1989, 54, 1055–1066.
   Web of Science ®Google Scholar
• Mikhailov, S.N.; Karpeisky, M.Ya. Nucleotide conformational analogs. V. Synthesis of 5′-C-methylnucleosides on the basis of 6-deoxy-D-allose. Bioorgan. Khim. (USSR) 1979, 5, 895–905.
   Web of Science ®Google Scholar
• Mikhailov, S.N.; Padyukova, N.Sh.; Struchkova, M.I.; Yarotsky, S.V. Synthesis and NMR spectra of some derivatives of methyl 6-deoxy-α;- and β;-D-allofuranosides and methyl 6-deoxy-α;- and β;-L-talofuranosides. Bioorgan. Khim. (USSR) 1982, 8, 926–931.
   Web of Science ®Google Scholar
• Padyukova, N.Sh.; Fomitcheva, M.V.; Mikhailov, S.N.; Janta-Lipinsky, M. Synthesis of thymidine 5′-derivatives. Bioorgan. Khim. (USSR) 1990, 16 (5), 668–673.
   PubMed Web of Science ®Google Scholar
• Mikhailov, S.N.; Grishko, N.B. Acyclic analogs of nucleosides. Synthesis of chiral 1,5-dihydroxy-4-methyl-3-oxapent-2-yl derivatives of uracil. Chem. Heterocyclic Compd. 1988, 24(1), 75–78.
   Google Scholar
• Wang, Y.; Hogenkamp, H.P.; Long, R.A.; Revankar, G.R.; Robins, R.K. A convenient synthesis of 5′-deoxyribonucleosides. Carbohydr. Res. 1977, 59, 449–457.
   Web of Science ®Google Scholar
• Lerner, L.M. Preparation of the enantiomeric forms of 9-(5, 6-dideoxy-. beta.-D-ribo-hex-5-enofuranosyl) adenine. J. Org. Chem. 1978, 43(12), 2469–2473.
   Web of Science ®Google Scholar
• Mikhailopulo, I.A.; Pricota, T.I.; Poopeiko, N.E.; Sivets, G.G.; Kvasyuk, E.I.; Sviryaeva, T.V.; Savochkina, L.P.; Beabealashvilli, R.S. 3′‐Fluoro‐3′‐deoxyribonucleoside 5′‐triphosphates: Synthesis and use as terminators of RNA biosynthesis. FEBS Lett. 1989, 250, 139–141.
   PubMed Web of Science ®Google Scholar
• Beigelman, L.N.; Gurskaya, G.V.; Tsapkina, E.N.; Mikhailov, S.N.().Epimerization during the acetolysis of 3-O-acetyl-5-O-benzoyl-1,2-O-isopropylidene-3-C-methyl-α-d-ribofuranose. Synthesis of 3′-C-methylnucleosides with the β-d-ribo-and α-d-arabino configurations. Carbohydr. Res. 1988, 181, 77–88.
   Web of Science ®Google Scholar
• Beigelman, L.N.; Ermolinsky, B.S.; Gurskaya, G.V.; Tsapkina, E.N.; Karpeisky, M.Y.; Mikhailov, S.N. New syntheses of 2′-C-methylnucleosides starting from D-glucose and D-ribose. Carbohydr. Res. 1987, 166, 219–232.
   Web of Science ®Google Scholar
• Esipov, R.S.; Gurevich, A.I.; Chuvikovsky, D.V.; Chupova, L.A.; Muravyova, T.I.; Miroshnikov, A.I. Overexpression of Escherichia coli genes encoding nucleoside phosphorylases in the pET/Bl21(DE3) system yields active recombinant enzymes. Protein Expres. Purif. 2002, 24, 56–60.
   PubMed Web of Science ®Google Scholar