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Ep 2516637 B1 (19) TZZ _¥_T (11) EP 2 516 637 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12N 9/10 (2006.01) C12P 19/38 (2006.01) 20.04.2016 Bulletin 2016/16 (86) International application number: (21) Application number: 10798096.3 PCT/EP2010/070581 (22) Date of filing: 22.12.2010 (87) International publication number: WO 2011/076894 (30.06.2011 Gazette 2011/26) (54) THERMOSTABLE BIOCATALYST COMBINATION FOR NUCLEOSIDE SYNTHESIS Wärmebeständige Biokatalysatorkombination zur Nukleotidsynthese Combinaison de biocatalyseur thermostable pour synthèse de nucléoside (84) Designated Contracting States: • TARAN S A ET AL: "Enzymatic AL AT BE BG CH CY CZ DE DK EE ES FI FR GB transglycosylation of natural and modified GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO nucleosides by immobilized thermostable PL PT RO RS SE SI SK SM TR nucleoside phosphorylases from Geobacillus stearothermophilus", RUSSIAN JOURNAL OF (30) Priority: 22.12.2009 EP 09382296 BIOORGANIC CHEMISTRY, vol. 35, no. 6, November 2009 (2009-11), pages 739-745, (43) Date of publication of application: XP002585194, 31.10.2012 Bulletin 2012/44 • TRELLES J A ET AL: "Screening of Catalytically Active Microorganisms for the Synthesis of (73) Proprietor: Plasmia Biotech, S.L. 6-Modified Purine Nucleosides", 08100 Mollet del Vallès (ES) BIOTECHNOLOGY LETTERS, KLUWER ACADEMIC PUBLISHERS, DO LNKD- (72) Inventors: DOI:10.1007/S10529-005-5628-7, vol. 27, no. 11, 1 • MONTILLA AREVALO, Rafael June 2005 (2005-06-01), pages 759-763, E-08100 Mollet del Vallès (ES) XP019230857, ISSN: 1573-6776 • DERONCELÉ THOMAS, Víctor, Manuel • DATABASE UniProt [Online] 1 November 1999 E-08100 Mollet del Vallès (ES) (1999-11-01), "SubName: Full=Uridine • LÓPEZ GÓMEZ, Cristina phosphorylase; EC=<A E-08100 Mollet del Vallès (ES) HREF="http://srs.ebi.ac.uk/srsbin/cgi-bin/ • PASCUAL GILABERT, Marta wgetz?[enzyme-ECNumber:2.4.2.3]+-e">2.4.2. E-08100 Mollet del Vallès (ES) 3</A>;", XP002585195, retrieved from EBI • ESTÉVEZ COMPANY, Carlos accession no. UNIPROT:Q9YA34 Database E-08100 Mollet del Vallès (ES) accession no. Q9YA34 & KAWARABAYASHI • CASTELLS BOLIART, Josep YUTAKA ET AL: "Complete genome sequence of E-08100 Mollet del Vallès (ES) an aerobic hyper-thermophilic crenarchaeon, aeropyrum pernix K1", DNA RESEARCH, (74) Representative: Oficina Ponti, SLP UNIVERSAL ACADEMY PRESS, JP LNKD- C. Consell de Cent, 322 DOI:10.1093/DNARES/6.2.83, vol. 6, no. 2, 1 08007 Barcelona (ES) January 1999 (1999-01-01) , pages 83-101, XP002957164, ISSN: 1340-2838 (56) References cited: WO-A1-95/16785 WO-A2-03/035012 US-A1- 2005 142 645 Note: Within nine months of the publication of the mention of the grant of the European patent in the European Patent Bulletin, any person may give notice to the European Patent Office of opposition to that patent, in accordance with the Implementing Regulations. Notice of opposition shall not be deemed to have been filed until the opposition fee has been paid. (Art. 99(1) European Patent Convention). EP 2 516 637 B1 Printed by Jouve, 75001 PARIS (FR) (Cont. next page) EP 2 516 637 B1 • HAMAMOTO TOMOKI ET AL: "Cloning of purine • CACCIAPUOTI GIOVANNA ET AL: "Purification nucleoside phosphorylase II gene from Bacillus and characterization of extremely thermophilic stearothermophilus TH 6-2 and characterization and thermostable 5’-methylthioadenosine of its gene product", BIOSCIENCE phosphorylase from the archaeon Sulfolobus BIOTECHNOLOGY AND BIOCHEMISTRY, vol. 61, solfataricus: Purine nucleoside phosphorylase no. 2, 1997, pages 276-280, XP002097506, ISSN: activity and evidence for intersubunit disulfide 0916-8451 cited in the application bonds", JOURNAL OF BIOLOGICAL • HAMAMOTO TOMOKI ET AL: "Cloning and CHEMISTRY, vol. 269, no. 40, 1994, pages expression of purine nucleoside phosphorylase 24762-24769, XP002625003, ISSN: 0021-9258 I gene from Bacillus stearothermophilus TH 6-2", • CACCIAPUOTI GIOVANNA ET AL: "Extremely BIOSCIENCE BIOTECHNOLOGY AND thermophilic and thermostable BIOCHEMISTRY, vol. 61, no. 2, 1997, pages 5’-methylthioadenosine phosphorylase from the 272-275, XP002097508, ISSN: 0916-8451 cited in archaeon Sulfolobus solfataricus: Gene cloning the application and amino acid sequence determination", • CACCIAPUOTI GIOVANNA ET AL: "Purine EUROPEAN JOURNAL OF BIOCHEMISTRY, vol. nucleoside phosphorylases from 239, no. 3, 1996, pages 632-637, XP002625004, hyperthermophilic Archaea require a CXC motif ISSN: 0014-2956 for stability and folding.", THE FEBS JOURNAL • FRANCIS E JENNEY JR ET AL: "The impact of OCT2009 LNKD- PUBMED:19740110, vol. 276, no. extremophiles on structural genomics (and vice 20, October 2009 (2009-10), pages 5799-5805, versa)", EXTREMOPHILES ; LIFE UNDER XP002585196, ISSN: 1742-4658 EXTREME CONDITIONS, SPRINGER-VERLAG, • CACCIAPUOTI GIOVANNA ET AL: "A novel TO, vol. 12, no. 1, 13 June 2007 (2007-06-13), hyperthermostable 5 ’-deoxy-5 pages 39-50, XP019593097, ISSN: 1433-4909 ’-methylthioadenosine phosphorylase from the • CACCIAPUOTI G ET AL: "Heterologous archaeon Sulfolobus solfataricus", FEBS Expression of 5’-Methylthioadenosine JOURNAL, vol. 272, no. 8, April 2005 (2005-04), Phosphorylase from the ArchaeonSulfolobus pages 1886-1899, XP002585197, cited in the solfataricus:Characterization of the application Recombinant Protein and Involvement of • CACCIAPUOTI GIOVANNA ET AL: "Biochemical Disulfide Bonds in Thermophilicity and and structural characterization of Thermostability", PROTEIN EXPRESSION AND mammalian-like purine nucleoside PURIFICATION, ACADEMIC PRESS, SAN DIEGO, phosphorylase from the Archaeon Pyrococcus CA, vol. 16, no. 1, 1 June 1999 (1999-06-01), pages furiosus", FEBS JOURNAL, vol. 274, no. 10, May 125-135, XP004441691, ISSN: 1046-5928, DOI: 2007 (2007-05), pages 2482-2495, XP002585198, 10.1006/PREP.1999.1076 cited in the application • DATABASE UniProt [Online] 1 October 2001 (2001-10-01), "SubName: Full=Purine nucleoside phosporylase (DeoD); EC=2.4.2.1;", XP002625014, retrieved from EBI accession no. UNIPROT:Q97Y30 Database accession no. Q97Y30 -& SHE QUNXIN ET AL: "The complete genome of the crenarchaeon Sulfolobus solfataricus P2", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 98, no. 14, 3 July 2001 (2001-07-03), pages 7835-7840, XP002625002, ISSN: 0027-8424 2 EP 2 516 637 B1 Description Field of the Invention 5 [0001] The invention belongs to the field of biotechnology. Background of the invention [0002] (Deoxy)nucleosides are glycosylamines consisting of a base like a purine or a pyrimidine bound to a ribose or 10 deoxyribose sugar, the latter being cyclic pentoses. Examples of these include cytidine, uridine, adenosine, guanosine, thymidine, and inosine. Nucleoside analogues are extensively used as antiviral and anticancer agents because of their ability to act as reverse transcriptase inhibitors or chain terminators in RNA or DNA synthesis [1]. [0003] Chemical synthesis of nucleoside analogues has been achieved stereoselectively but using expensive or pol- luting reagents [2] and involving multistage processes that can be time consuming. Biocatalytic procedures offer a good 15 alternative to the chemical synthesis of nucleosides because biocatalyzed reactions are regio- and stereoselective and allow the decrease of by-products content. Of particular interest within the biocatalytic procedures is the enzymatic transglycosylation between a sugar-donating nucleoside and an acceptor base by means of enzymes that catalyse the general reversible reactions [3] as depicted in Figures 1 and 2. [0004] Nucleoside phosphorylases are transferases widely distributed in mammalian cells and bacteria and play a 20 central role in the nucleoside metabolism salvage pathway. They have a dual functionality. On the one hand, they catalyse the reversible cleavage of the glycosidic bond of ribo- or deoxyribo nucleosides in the presence of inorganic phosphate in order to generate the base and ribose- or deoxyribose-1-phosphate. These enzymatic reactions employing the purine nucleoside phosphorylases and the pyrimidine nucleoside phosphorylases are shown in Figure 1. On the other hand, these enzymes catalyse phosphate-dependent pentose transfer between purine or pyrimidine bases and 25 nucleosides, i.e. transglycosylation reactions, to produce nucleosides with differing bases. Figure 2 shows an example of a one-pot synthesis using nucleoside phosphorylases. [0005] When the pyrimidine and purine nucleoside phosphorylases are used in combination, it is possible to transfer the sugar from a donor pyrimidine nucleoside to a purine or pyrimidine acceptor base as well as from a donor purine nucleoside to a pyrimidine or purine acceptor base, depending on the starting materials used [4]. As a consequence, 30 nucleoside phosphorylases from different sources, mainly bacterial, have been exploited as tools for the enzymatic synthesis of nucleoside analogues. [0006] In nature these enzymes have been described in various microbial strains, particularly in thermophilic bacteria (i.e. bacteria thriving at temperatures between 45 °C and 80 °C), which have been used as sources of nucleoside phosphorylases in numerous works for obtaining modified nucleosides by enzymatic transglycosylation. However, al- 35 though in these studies the target products yields were sufficiently high, the amount or ratio of the enzymatic activities necessary for transglycosylation was non-optimal [5]. They required either a considerable extension in the reaction time (up to several days) or an increase in
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