Structural and functional characterization of thermostable biocatalysts for the synthesis of 6-aminopurine nucleoside-5′-monophospate analogues
The present work describes the functional and structural characterization of adenine phosphoribosyltransferase 2 from thermus thermophilus hb8 (ttaprt2). The combination of structural and substrate specificity data provided valuable information for immobilization studies. Dimeric ttaprt2 was immobil...
- Autores:
-
Del Arco, Jon
Pérez, Elena
Naitow, Hisashi
Matsuura, Yoshinori
Kunishima, Naoki
Fernández-Lucas, Jesús
- Tipo de recurso:
- Article of journal
- Fecha de publicación:
- 2019
- Institución:
- Corporación Universidad de la Costa
- Repositorio:
- REDICUC - Repositorio CUC
- Idioma:
- eng
- OAI Identifier:
- oai:repositorio.cuc.edu.co:11323/3330
- Acceso en línea:
- https://hdl.handle.net/11323/3330
https://repositorio.cuc.edu.co/
- Palabra clave:
- Thermophiles
Biocatalysis
Enzyme immobilization
Protein crystallography
Termofilos
Biocatálisis
Inmovilización de enzimas
Cristalografia de proteinas
- Rights
- openAccess
- License
- Attribution-NonCommercial-ShareAlike 4.0 International
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|
dc.title.spa.fl_str_mv |
Structural and functional characterization of thermostable biocatalysts for the synthesis of 6-aminopurine nucleoside-5′-monophospate analogues |
dc.title.translated.spa.fl_str_mv |
Caracterización estructural y funcional de biocatalizadores termoestables para la síntesis de análogos del nucleósido 5'-monofosfato de 6-aminopurina. |
title |
Structural and functional characterization of thermostable biocatalysts for the synthesis of 6-aminopurine nucleoside-5′-monophospate analogues |
spellingShingle |
Structural and functional characterization of thermostable biocatalysts for the synthesis of 6-aminopurine nucleoside-5′-monophospate analogues Thermophiles Biocatalysis Enzyme immobilization Protein crystallography Termofilos Biocatálisis Inmovilización de enzimas Cristalografia de proteinas |
title_short |
Structural and functional characterization of thermostable biocatalysts for the synthesis of 6-aminopurine nucleoside-5′-monophospate analogues |
title_full |
Structural and functional characterization of thermostable biocatalysts for the synthesis of 6-aminopurine nucleoside-5′-monophospate analogues |
title_fullStr |
Structural and functional characterization of thermostable biocatalysts for the synthesis of 6-aminopurine nucleoside-5′-monophospate analogues |
title_full_unstemmed |
Structural and functional characterization of thermostable biocatalysts for the synthesis of 6-aminopurine nucleoside-5′-monophospate analogues |
title_sort |
Structural and functional characterization of thermostable biocatalysts for the synthesis of 6-aminopurine nucleoside-5′-monophospate analogues |
dc.creator.fl_str_mv |
Del Arco, Jon Pérez, Elena Naitow, Hisashi Matsuura, Yoshinori Kunishima, Naoki Fernández-Lucas, Jesús |
dc.contributor.author.spa.fl_str_mv |
Del Arco, Jon Pérez, Elena Naitow, Hisashi Matsuura, Yoshinori Kunishima, Naoki Fernández-Lucas, Jesús |
dc.subject.spa.fl_str_mv |
Thermophiles Biocatalysis Enzyme immobilization Protein crystallography Termofilos Biocatálisis Inmovilización de enzimas Cristalografia de proteinas |
topic |
Thermophiles Biocatalysis Enzyme immobilization Protein crystallography Termofilos Biocatálisis Inmovilización de enzimas Cristalografia de proteinas |
description |
The present work describes the functional and structural characterization of adenine phosphoribosyltransferase 2 from thermus thermophilus hb8 (ttaprt2). The combination of structural and substrate specificity data provided valuable information for immobilization studies. Dimeric ttaprt2 was immobilized onto glutaraldehydeactivated magresyn®amine magnetic iron oxide porous microparticles by two different strategies: a) an enzyme immobilization at ph 8.5 to encourage the immobilization process by n-termini (mttaprt2a, mttaprt2b, mttaprt2c) or b) an enzyme immobilization at ph 10.0 to encourage the immobilization process through surface exposed lysine residues (mttaprt2d, mttaprt2e, mttaprt2f). According to catalyst load experiments, mttaprt2b (activity: 480 iu g−1 biocatalyst, activity recovery: 52%) and mttaprt2f (activity: 507 iu g−1 biocatalyst, activity recovery: 44%) were chosen as optimal derivatives. The biochemical characterization studies demonstrated that immobilization process improved the thermostability of ttaprt2. Moreover, the potential reusability of mttaprt2b and mttaprt2f was also tested. Finally, mttaprt2f was employed in the synthesis of nucleoside-5′-monophosphate analogues. |
publishDate |
2019 |
dc.date.accessioned.none.fl_str_mv |
2019-05-15T12:59:05Z |
dc.date.available.none.fl_str_mv |
2019-05-15T12:59:05Z |
dc.date.issued.none.fl_str_mv |
2019-01-03 |
dc.type.spa.fl_str_mv |
Artículo de revista |
dc.type.coar.fl_str_mv |
http://purl.org/coar/resource_type/c_2df8fbb1 |
dc.type.coar.spa.fl_str_mv |
http://purl.org/coar/resource_type/c_6501 |
dc.type.content.spa.fl_str_mv |
Text |
dc.type.driver.spa.fl_str_mv |
info:eu-repo/semantics/article |
dc.type.redcol.spa.fl_str_mv |
http://purl.org/redcol/resource_type/ART |
dc.type.version.spa.fl_str_mv |
info:eu-repo/semantics/acceptedVersion |
format |
http://purl.org/coar/resource_type/c_6501 |
status_str |
acceptedVersion |
dc.identifier.uri.spa.fl_str_mv |
https://hdl.handle.net/11323/3330 |
dc.identifier.instname.spa.fl_str_mv |
Corporación Universidad de la Costa |
dc.identifier.reponame.spa.fl_str_mv |
REDICUC - Repositorio CUC |
dc.identifier.repourl.spa.fl_str_mv |
https://repositorio.cuc.edu.co/ |
url |
https://hdl.handle.net/11323/3330 https://repositorio.cuc.edu.co/ |
identifier_str_mv |
Corporación Universidad de la Costa REDICUC - Repositorio CUC |
dc.language.iso.none.fl_str_mv |
eng |
language |
eng |
dc.relation.references.spa.fl_str_mv |
Adams, P.D., Grosse-Kunstleve, R.W., Hung, L.W., Ioerger, T.R., McCoy, A.J., Moriarty, N.W., Read, R.J., Sacchettini, J.C., Sauter, N.K., Terwilliger, T.C., 2002. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D Biol. Crystallogr. 58, 1948–1954. Baba, S., Hoshino, T., Ito, L., Kumasaka, T., 2013. Humidity control and hydrophilic glue coating applied to mounted protein crystals improves X-ray diffraction experiments. Acta Crystallogr. D Biol. Crystallogr. 69, 1839–1849. Barbosa, O., Ortiz, C., Berenguer-Murcia, Á., Torres, R., Rodrigues, R.C., FernandezLafuente, R., 2014. Glutaraldehyde in bio-catalysts design: A useful crosslinker and a versatile tool in enzyme immobilization. RSC Adv. 4, 1583–1600. Barbosa, O., Ortiz, C., Berenguer-Murcia, Á., Torres, R., Rodrigues, R.C., FernandezLafuente, R., 2015. Strategies for the one-step immobilization-purification of enzymes as industrial biocatalysts. Biotechnol. Adv. 33 (5), 435–456. Berendsen, W.R., Lapin, A., Reuss, M., 2006. Investigations of reaction kinetics for immobilized enzymes—identification of parameters in the presence of diffusion limitation. Biotechnol. Prog. 22 (5), 1305–1312. Chapman, J., Ismail, A., Dinu, C., 2018. Industrial applications of enzymes: Recent advances, techniques, and outlooks. Catalysts 8 (6), 238. De Clercq, E., 2005. Recent highlights in the development of new antiviral drugs. Curr. Opin. Microbiol. 8 (5), 552–560. Del Arco, J., Fernández-Lucas, J., 2017. Purine and pyrimidine phosphoribosyltransferases: a versatile tool for enzymatic synthesis of nucleoside-5'-monophosphates. Curr. Pharm. Des. 23 (45), 6898–6912. Del Arco, J., Cejudo-Sanches, J., Esteban, I., Clemente-Suárez, V.J., Hormigo, D., Perona, A., Fernández-Lucas, J., 2017. Enzymatic production of dietary nucleotides from lowsoluble purine bases by an efficient, thermostable and alkali-tolerant biocatalyst. Food Chem. 237, 605–611. Del Arco, J., Fernández-Lucas, J., 2018. Purine and pyrimidine salvage pathway in thermophiles: a valuable source of biocatalysts for the industrial production of nucleic acid derivatives. Appl. Microbiol. Biotechnol. 102 (18), 7805–7820. Del Arco, J., Acosta, J., Pereira, H.M., Perona, A., Lokanath, N.K., Kunishima, N., Fernández-Lucas, J., 2018a. Enzymatic production of non-natural nucleoside-5’- monophosphates by a novel thermostable uracil phosphoribosyltransferase. ChemCatChem 10 (2), 439–448. Del Arco, J., Martínez-Pascual, S., Clemente-Suárez, V.J., Corral, O.J., Jordaan, J., Hormigo, D., Perona, A., Fernández-Lucas, J., 2018b. One-pot, one-step production of dietary nucleotides by magnetic biocatalysts. Catalysts 8 (5), 184. Del Arco, J., Martinez, M., Donday, M., Clemente-Suarez, V.J., Fernández-Lucas, J., 2018c. Cloning, expression and biochemical characterization of xanthine and adenine phosphoribosyltransferases from Thermus thermophilus HB8. Biocatal. Biotransform. 36 (3), 216–223. DeLano, W.L., 2002. The PyMOL Molecular Graphics System. Available online. http:// www.pymol.org. Dumorne, K., Córdova, D.C., Astorga-Eló, M., Renganathan, P., 2017. Extremozymes: a potential source for industrial applications. J. Microbiol. Biotechnol. 27 (4), 649–659. Elleuche, S., Schroder, C., Sahm, K., Antranikian, G., 2014. Extremozymes-biocatalysts with unique properties from extremophilic microorganisms. Curr. Opin. Biotechnol. 29, 116–123. Emsley, P., Cowtan, K., 2004. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132. Esipov, R.S., Timofeev, V.I., Sinitsyna, E.V., Tuzova, E.S., Esipova, L.V., Kostromina, M.A., Kuranova, I.P., Miroshnikov, A.I., 2018. Three-dimensional structure of recombinant adenine phosphoribosyltransferase from thermophilic bacterial strain Thermus thermophilus HB27. Russ. J. Bioorg. Chem. 44, 504–510. Galmarini, C.M., Mackey, J.R., Dumontet, C., 2002. Nucleoside analogues and nucleobases in cancer treatment. Lancet Oncol. 3 (7), 415–424. Gill, S.C., Von Hippel, P.H., 1989. Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182, 319–326. Inouye, K., Kuzuya, K., Tonomura, B.I., 1998. Sodium chloride enhances markedly the thermal stability of thermolysin as well as its catalytic activity. Biochim. Biophys. Acta (BBA) Protein Struct. Mol. Enzym. 1388 (1), 209–214. Jemli, S., Ayadi-Zouari, D., Hlima, H.B., Bejar, S., 2016. Biocatalysts: application and engineering for industrial purposes. Crit. Rev. Biotechnol. 36 (2), 246–258. Kabsch, W., 1976. A solution for best rotation to relate two sets of vectors. Acta Crystallogr. A 32, 922–923. Klein, M.P., Nunes, M.R., Rodrigues, R.C., Benvenutti, E.V., Costa, T.M., Hertz, P.F., Ninow, J.L., 2012. Effect of the support size on the properties of β-galactosidase immobilized on chitosan: advantages and disadvantages of macro and nanoparticles. Biomacromolecules 13 (8), 2456–2464. Li, S., Chen, L., Hu, Y., Fang, G., Zhao, M., Guo, Y., Pang, Z., 2017. Enzymatic production of 5′-inosinic acid by AMP deaminase from a newly isolated Aspergillus oryzae. Food Chem. 216, 275–281. Liu, C., Saeki, D., Matsuyama, H., 2017. A novel strategy to immobilize enzymes on microporous membranes via dicarboxylic acid halides. RSC Adv. 7 (76), 48199–48207. Liu, Z.Q., Zhang, L., Sun, L.H., Li, X.J., Wan, N.W., Zheng, Y.G., 2012. Enzymatic production of 5′-inosinic acid by a newly synthesised acid phosphatase/phosphotransferase. Food Chem. 134 (2), 948–956. Mateo, C., Palomo, J.M., Fernández-Lorente, G., Guisán, J.M., Fernández-Lafuente, R., 2007. Improvement of enzyme activity, stability and selectivity via immobilization techniques. Enzyme Microb. Technol. 40 (6), 1451–1463. Murakami, Y., Hoshi, R., Hirata, A., 2003. Characterization of polymer–enzyme complex as a novel biocatalyst for nonaqueous enzymology. J. Mol. Catal. 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Bioprospecting of extremophiles for biotechnology applications. In: Sani, R.K., Rathinam, N.K. (Eds.), Extremophilic Microbial Processing of Lignocellulosic Feedstocks to Biofuels, Value-Added Products, and Usable Power. Springer, Berlin, pp. 1–23. Rehse, P.H., Tahirov, T.H., 2005. Crystal structure of a purine/pyrimidine phosphoribosyltransferase-related protein from Thermus thermophilus HB8. Proteins 61,658–665. Rodrigues, R.C., Ortiz, C., Berenguer-Murcia, A., Torres, R., Fernández-Lafuente, R., 2013. Modifying enzyme activity and selectivity by immobilization. Chem. Soc. Rev. 42 (15), 6290–6307. Scism, R.A., Stec, D.F., Bachmann, B.O., 2007. Synthesis of nucleotide analogues by a promiscuous phosphoribosyltransferase. Org. Lett. 9 (21), 4179–4182. Serra, I., Conti, S., Piškur, J., Clausen, A.R., Munch-Petersen, B., Terreni, M., Ubiali, D., 2014. Immobilized Drosophila melanogaster deoxyribonucleoside kinase (DmdNK) as a high performing biocatalyst for the synthesis of purine arabinonucleotides. Adv. Synth. Catal. 356 (2–3), 563–570. Shi, W., Tanaka, K.S., Crother, T.R., Taylor, M.W., Almo, S.C., Schramm, V.L., 2001. Structural analysis of adenine phosphoribosyltransferase from Saccharomyces cerevisiae. Biochemistry 40 (36), 10800–10809. Shi, W., Sarver, A.E., Wang, C.C., Tanaka, K.S., Almo, S.C., Schramm, V.L., 2002. Closedsite complexes of adenine phosphoribosyltransferase from Giardia lamblia reveal a mechanism of ribosyl migration. J. Biol. Chem. 277 (42), 39981–39988. Shrestha, N., Chilkoor, G., Vemuri, B., Rathinam, N., Sani, R.K., Gadhamshetty, V., 2018. Extremophiles for microbial-electrochemistry applications: a critical review. Bioresour. Technol. 255, 318–330. Silva, M., Silva, C.H., Iulek, J., 2004. Thiemann OH. Three-dimensional structure of human adenine phosphoribosyltransferase and its relation to DHA-urolithiasis. Biochemistry 43 (24), 7663–7671. Sin, I.L., Finch, L.R., 1972. Adenine phosphoribosyltransferase in Mycoplasma mycoides and Escherichia coli. J. Bacteriol. 112 (1), 439–444. Tuttle, J.V., Krenitsky, T.A., 1980. Purine phosphoribosyltransferases from Leishmania donovani. J. Biol. Chem. 235 (3), 909–916. Winn, M., Ballard, C., Cowtan, K., Dodson, E., Emsley, P., Evans, P., Keegan, R., Krissinel, E., Leslie, A., McCoy, A., McNicholas, S., Murshudov, G., Pannu, N., Potterton, E., Powell, H., Read, R., Vagin, A., Wilson, K., 2011. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235–242. Zhao, X.S., Bao, X.Y., Guo, W., Lee, F.Y., 2006. Immobilizing catalysts on porous materials. Mater. Today 9 (3), 32–39. Zou, H., Cai, G., Cai, W., Li, H., Gu, Y., Park, Y., Meng, F., 2008. Extraction and DNA digestion of 5′-phosphodiesterase from malt root. Tsinghua Sci. Technol. 13 (4), 480–484. Zucca, P., Sanjust, E., 2014. Inorganic materials as supports for covalent enzyme immobilization: Methods and mechanisms. Molecules 19 (9), 14139–14194 |
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Del Arco, JonPérez, ElenaNaitow, HisashiMatsuura, YoshinoriKunishima, NaokiFernández-Lucas, Jesús2019-05-15T12:59:05Z2019-05-15T12:59:05Z2019-01-03https://hdl.handle.net/11323/3330Corporación Universidad de la CostaREDICUC - Repositorio CUChttps://repositorio.cuc.edu.co/The present work describes the functional and structural characterization of adenine phosphoribosyltransferase 2 from thermus thermophilus hb8 (ttaprt2). The combination of structural and substrate specificity data provided valuable information for immobilization studies. Dimeric ttaprt2 was immobilized onto glutaraldehydeactivated magresyn®amine magnetic iron oxide porous microparticles by two different strategies: a) an enzyme immobilization at ph 8.5 to encourage the immobilization process by n-termini (mttaprt2a, mttaprt2b, mttaprt2c) or b) an enzyme immobilization at ph 10.0 to encourage the immobilization process through surface exposed lysine residues (mttaprt2d, mttaprt2e, mttaprt2f). According to catalyst load experiments, mttaprt2b (activity: 480 iu g−1 biocatalyst, activity recovery: 52%) and mttaprt2f (activity: 507 iu g−1 biocatalyst, activity recovery: 44%) were chosen as optimal derivatives. The biochemical characterization studies demonstrated that immobilization process improved the thermostability of ttaprt2. Moreover, the potential reusability of mttaprt2b and mttaprt2f was also tested. Finally, mttaprt2f was employed in the synthesis of nucleoside-5′-monophosphate analogues.El presente trabajo describe la caracterización funcional y estructural de la adenina fosforribosiltransferasa 2 de thermus thermophilus hb8 (ttaprt2). La combinación de datos de especificidad estructural y de sustrato proporcionó información valiosa para los estudios de inmovilización. El ttaprt2 dimérico se inmovilizó en micropartículas porosas de óxido de hierro magnético magresyn®amine activado con glutaraldehido mediante dos estrategias diferentes: a) una inmovilización de enzima a ph 8.5 para alentar el proceso de inmovilización por n-termini (mttaprt2a, mttaprt2c) o bttaprt2c) o b) ph 10.0 para fomentar el proceso de inmovilización a través de residuos de lisina expuestos en la superficie (mttaprt2d, mttaprt2e, mttaprt2f). De acuerdo con los experimentos de carga de catalizador, mttaprt2b (actividad: 480 iu g − 1 biocatalizador, recuperación de actividad: 52%) y mttaprt2f (actividad: 507 iu g − 1 biocatalizador, recuperación de actividad: 44%) fueron elegidos como derivados óptimos. Los estudios de caracterización bioquímica demostraron que el proceso de inmovilización mejoró la termoestabilidad de ttaprt2. Además, también se probó la reutilización potencial de mttaprt2b y mttaprt2f. Finalmente, mttaprt2f se empleó en la síntesis de análogos de nucleósido-5'-monofosfato.Del Arco, Jon-c5ed68af-857c-4b28-99a7-33a4254ed926-0Pérez, Elena-e0e56b28-2fe8-4d52-bb25-104505765b55-0Naitow, Hisashi-e516c1df-173a-440b-a5c0-570c4e8faffd-0Matsuura, Yoshinori-39696af8-8ded-4e90-b8e0-c840a19ce1f9-0Kunishima, Naoki-6baf4ae0-b84a-4faf-b26f-66d30cc43d7a-0Fernández-Lucas, Jesús-454d03d3-2cec-45b1-a796-51012f85b786-0engUniversidad de la CostaAttribution-NonCommercial-ShareAlike 4.0 Internationalhttp://creativecommons.org/licenses/by-nc-sa/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2ThermophilesBiocatalysisEnzyme immobilizationProtein crystallographyTermofilosBiocatálisisInmovilización de enzimasCristalografia de proteinasStructural and functional characterization of thermostable biocatalysts for the synthesis of 6-aminopurine nucleoside-5′-monophospate analoguesCaracterización estructural y funcional de biocatalizadores termoestables para la síntesis de análogos del nucleósido 5'-monofosfato de 6-aminopurina.Artículo de revistahttp://purl.org/coar/resource_type/c_6501http://purl.org/coar/resource_type/c_2df8fbb1Textinfo:eu-repo/semantics/articlehttp://purl.org/redcol/resource_type/ARTinfo:eu-repo/semantics/acceptedVersionAdams, P.D., Grosse-Kunstleve, R.W., Hung, L.W., Ioerger, T.R., McCoy, A.J., Moriarty, N.W., Read, R.J., Sacchettini, J.C., Sauter, N.K., Terwilliger, T.C., 2002. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D Biol. Crystallogr. 58, 1948–1954. Baba, S., Hoshino, T., Ito, L., Kumasaka, T., 2013. Humidity control and hydrophilic glue coating applied to mounted protein crystals improves X-ray diffraction experiments. Acta Crystallogr. D Biol. Crystallogr. 69, 1839–1849. Barbosa, O., Ortiz, C., Berenguer-Murcia, Á., Torres, R., Rodrigues, R.C., FernandezLafuente, R., 2014. Glutaraldehyde in bio-catalysts design: A useful crosslinker and a versatile tool in enzyme immobilization. RSC Adv. 4, 1583–1600. Barbosa, O., Ortiz, C., Berenguer-Murcia, Á., Torres, R., Rodrigues, R.C., FernandezLafuente, R., 2015. Strategies for the one-step immobilization-purification of enzymes as industrial biocatalysts. Biotechnol. Adv. 33 (5), 435–456. Berendsen, W.R., Lapin, A., Reuss, M., 2006. Investigations of reaction kinetics for immobilized enzymes—identification of parameters in the presence of diffusion limitation. Biotechnol. Prog. 22 (5), 1305–1312. Chapman, J., Ismail, A., Dinu, C., 2018. Industrial applications of enzymes: Recent advances, techniques, and outlooks. Catalysts 8 (6), 238. De Clercq, E., 2005. Recent highlights in the development of new antiviral drugs. Curr. Opin. Microbiol. 8 (5), 552–560. Del Arco, J., Fernández-Lucas, J., 2017. Purine and pyrimidine phosphoribosyltransferases: a versatile tool for enzymatic synthesis of nucleoside-5'-monophosphates. Curr. Pharm. Des. 23 (45), 6898–6912. Del Arco, J., Cejudo-Sanches, J., Esteban, I., Clemente-Suárez, V.J., Hormigo, D., Perona, A., Fernández-Lucas, J., 2017. Enzymatic production of dietary nucleotides from lowsoluble purine bases by an efficient, thermostable and alkali-tolerant biocatalyst. Food Chem. 237, 605–611. Del Arco, J., Fernández-Lucas, J., 2018. 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