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Serine Hydroxymethyltransferase from Streptococcus Thermophilus and Halohydrine Dehalogenase D2 from Gammaproteobacterium

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Serine Hydroxymethyltransferase from Streptococcus Thermophilus and Halohydrine Dehalogenase D2 from Gammaproteobacterium Insight into the structure and function of engineered biocatalysts: serine hydroxymethyltransferase from Streptococcus thermophilus and halohydrine dehalogenase D2 from Gammaproteobacterium Giovanna Petrillo ADVERTIMENT. La consulta d’aquesta tesi queda condicionada a l’acceptació de les següents condicions d'ús: La difusió d’aquesta tesi per mitjà del servei TDX (www.tdx.cat) i a través del Dipòsit Digital de la UB (diposit.ub.edu) ha estat autoritzada pels titulars dels drets de propietat intel·lectual únicament per a usos privats emmarcats en activitats d’investigació i docència. No s’autoritza la seva reproducció amb finalitats de lucre ni la seva difusió i posada a disposició des d’un lloc aliè al servei TDX ni al Dipòsit Digital de la UB. No s’autoritza la presentació del seu contingut en una finestra o marc aliè a TDX o al Dipòsit Digital de la UB (framing). Aquesta reserva de drets afecta tant al resum de presentació de la tesi com als seus continguts. En la utilització o cita de parts de la tesi és obligat indicar el nom de la persona autora. ADVERTENCIA. La consulta de esta tesis queda condicionada a la aceptación de las siguientes condiciones de uso: La difusión de esta tesis por medio del servicio TDR (www.tdx.cat) y a través del Repositorio Digital de la UB (diposit.ub.edu) ha sido autorizada por los titulares de los derechos de propiedad intelectual únicamente para usos privados enmarcados en actividades de investigación y docencia. No se autoriza su reproducción con finalidades de lucro ni su difusión y puesta a disposición desde un sitio ajeno al servicio TDR o al Repositorio Digital de la UB. No se autoriza la presentación de su contenido en una ventana o marco ajeno a TDR o al Repositorio Digital de la UB (framing). Esta reserva de derechos afecta tanto al resumen de presentación de la tesis como a sus contenidos. En la utilización o cita de partes de la tesis es obligado indicar el nombre de la persona autora. WARNING. On having consulted this thesis you’re accepting the following use conditions: Spreading this thesis by the TDX (www.tdx.cat) service and by the UB Digital Repository (diposit.ub.edu) has been authorized by the titular of the intellectual property rights only for private uses placed in investigation and teaching activities. Reproduction with lucrative aims is not authorized nor its spreading and availability from a site foreign to the TDX service or to the UB Digital Repository. Introducing its content in a window or frame foreign to the TDX service or to the UB Digital Repository is not authorized (framing). Those rights affect to the presentation summary of the thesis as well as to its contents. In the using or citation of parts of the thesis it’s obliged to indicate the name of the author. ! ! UNIVERSITAT DE BARCELONA (UB) Faculty of Pharmacy and Food Sciences INSTITUTE OF ADVANCED CHEMISTRY OF CATALONIA(IQAC) Department of Biological Chemistry and Molecular Modelling MOLECULAR BIOLOGY INSTITUTE OF BARCELONA (IBMB) Structural Biology Unit (SBU) BIOCHEMIZE S.L. Insight into the structure and function of engineered biocatalysts: serine hydroxymethyltransferase from Streptococcus thermophilus and halohydrine dehalogenase D2 from Gammaproteobacterium Giovanna Petrillo 2017 ! UNIVERSITAT DE BARCELONA FACULTAT DE FARMÀCIA I CIÈNCIES DE L’ALIMENTACIÓ Industrial PhD Program in Biotechnology 2013-2014. Departement of Biochemistry and Molecular Biology, Faculty of Pharmaceutics, University of Barcelona (UB) Insight into the structure and function of engineered biocatalysts: serine hydroxymethyltransferase from Streptococcus thermophilus and halohydrine dehalogenase D2 from Gammaproteobacterium Doctoral thesis presented by Giovanna Petrillo, B.S degree in Biotechnology, for the degree of Industrial PhD from University of Barcelona. PhD student: Giovanna Petrillo Thesis supervisor: Thesis co-supervisor : Prof. Pere Clapés Saborit Prof. Isabel Usón Finkenzeller Thesis tutor: Thesis company tutor: Prof. Josefa Badia Palacín Dr. Jaume Mir Martinez Barcelona, 2017 Ai miei genitori e ai miei fratelli, colonne portanti ad Alfo, mattoni di questa costruzione, che è la mia vita. Acknowledgements First, I would like to thank my supervisors Prof. Pere Clapés from the Institute of Advanced Chemistry of Catalonia (IQAC) and Prof. Isabel Usón, from the Institute of Molecular Biology of Barcelona (IBMB), without whom none of this would have been possible. I thank them for all their help and guidance regarding this whole process and for their patience and dedication. I would also like to thank my company tutor, Dr. Jaume Mir Martinez, CEO of Biochemize. I would like to thank all the members of my lab, Massimo and Claudia for their support and enriching discussion, and all the new and old members I met over these years. Not forgetting the people from CRI3, CRI6 and CRI7: their suggestions and encouragement were valuable contributions to my project. I would like to thank Anna Cuppi, my collegue, flatmate and friend, who has always been a great support. Great thanks go to Karel and Raquel from Biotransformation and Bioactive molecules group of IQAC. They gave me a lot of support with complicated chemical “stuff”. Ringrazio Ivan, che mi ha regalato un’opportunità, tirandomi fuori dal grigiore e riservandomi un posto al sole di Barcellona e della sua amicizia. Ringrazio, uno ad uno gli "Amigos de D10S", la mia famiglia qui a Barcellona. Ringrazio te, Alfo, con il quale questa avventura è iniziata, con il quale gran parte delle cose belle della mia vita sono iniziate… dovunque fioriranno le viole, affonderano sempre le loro radici in un terreno coltivato con sincerità, rispetto e amore. Desidero, infine, ringraziare la mia famiglia per l’appoggio incondizionato e la stima, che sono un flusso incessante, come il mare. Contents Contents Abstract ....................................................................................................... 1 Frequently used abbreviations .................................................................... 3 General Introduction ................................................................................... 7 1. Enzymes, a brief overview ............................................................... 9 1.1. Enzymes and their early use in biotechnology ............................ 9 1.2. Enzyme chemistry: catalytic site, mechanism and cofactors .... 10 1.3. Enzyme selectivity ..................................................................... 14 2.1. Biocatalysis for industrial production of chemicals .................. 15 3. Biocatalyst engineering .................................................................. 16 4. Structural enzymology ................................................................... 17 4.1. X-ray crystallography as a method to design new biocatalysts . 19 Objectives ................................................................................................. 21 CHAPTER I .............................................................................................. 25 Introduction ........................................................................................ 27 1.1. Pyridoxal 5’-phosphate (PLP) and PLP-dependent enzymes .... 29 Figure 2: Structure of B6 vitamers ....................................................... 29 1.2. Structural diversity within PLP-dependent enzymes with emphasis on fold type I ..................................................................... 32 1.2.1 A common catalytic mechanism .............................................. 35 1.3 Serine hydroxymethyltransferase (SHMT), a fold type I PLP- dependent enzyme ............................................................................ 38 1.3.1 SHMT catalytic mechanism, details ........................................ 40 1.4 SHMT industrial and pharmaceutical applications .................... 43 1.4.1. SHMT as a biocatalysist ......................................................... 43 1.4.2. SHMT as a drug target ........................................................... 44 1.5 Serine hydroxymethyltransferase from Streptococcus thermophilus ..................................................................................... 48 Results and Discussion ....................................................................... 55 1.6 SHMTSth: overexpression and purification of wild-type and variants ............................................................................................. 57 I Contents 1.7 SHMTSth wild-type ...................................................................... 59 1.7.1 Crystallization and data collection of SHMTSth wild-type ....... 59 1.7.2 SHMTSth wild-type data processing, crystal structure solution and refinement .................................................................................. 60 1.8 SHMTSth Y55S and Y55T variants ............................................. 64 1.8.1 Crystallization and data collection of SHMTSth Y55S and Y55T variants ............................................................................................. 64 1.8.2 Data processing, crystal structure solution and refinement of SHMTSth Y55S and Y55T variants ................................................... 67 1.9 SHMTSth wild-type structures ..................................................... 70 1.9.1 SHMTSth wild-type apo-form (WTapo) overall structure ........ 70 1.9.1.1 SHMTSth wild-type apo-form catalytic site architecture ....... 74 1.9.2 Overall structure of SHMTSth wild-type binary complexes (WTgly and WTLThr ) ....................................................................
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