University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2017 Structural And Functional Studies Of Two Bacterial Terpene Cyclases: Geosmin Synthase And Epi-Isozizaene Synthase Golda Harris Barrow University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Biochemistry Commons, and the Chemistry Commons Recommended Citation Barrow, Golda Harris, "Structural And Functional Studies Of Two Bacterial Terpene Cyclases: Geosmin Synthase And Epi-Isozizaene Synthase" (2017). Publicly Accessible Penn Dissertations. 2181. https://repository.upenn.edu/edissertations/2181 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/2181 For more information, please contact [email protected]. Structural And Functional Studies Of Two Bacterial Terpene Cyclases: Geosmin Synthase And Epi-Isozizaene Synthase Abstract Terpene cyclases convert acyclic isoprenoid precursors into complex cyclic terpenoid compounds. Hydrophobic active site contours in terpene cyclases direct cyclization reactions through a cascade of carbocation intermediates by serving as templates for terpenoid product structure. Both local molecular structure at the active site and global protein structure encompassing domain organization and oligomerization state have effects on catalytic function in terpene cyclases. The goal of this work is characterization of the effects of local structural changes to the active site of a terpene cyclase, and a thorough understanding of the structure-function relationship of active site structure and domain organization in two terpene cyclases, geosmin synthase (ScGS) and epi-isozizaene synthase (EIZS) from Streptomyces coelicolor. Geosmin synthase (ScGS) is a bifunctional class I sesquiterpene cyclase that catalyzes the conversion of FPP to germacradienol, germacrene D, and geosmin in unique cyclization and cyclization-fragmentation reactions occurring in separate active sites. We determined the X-ray crystal structure of the N-terminal domain of ScGS and homology models of the C-terminal domain of ScGS, and used small-angle X-ray scattering (SAXS) to propose models of domain association in this system. Product analysis by gas chromatography-mass spectrometry (GC-MS) in this system indicates residues that are important for catalysis in the C-terminal domain cyclization-fragmentation reaction. EIZS is a promiscuous terpene cyclase and produces epi-isozizaene as a major product, along with five other sesquiterpene products. Single mutations at the active site of EIZS can drastically change the proportions and identities of sesquiterpene products. Mutagenesis of key residues at the active site to polar side chains results in mutant EIZS enzymes with altered catalytic properties. The X-ray crystal structures of EIZS F95N and F95C were determined and demonstrate that EIZS mutants containing polar residues at the active site do not exhibit global structural changes when compared to the wild type enzyme. GC-MS was used to analyze the products of eight new EIZS mutants, demonstrating formation of thirteen new sesquiterpene products not previously observed in this system. These results demonstrate that polar mutations are structurally and catalytically tolerated at the active site of EIZS. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Chemistry First Advisor David W. Christianson Keywords SAXS, terpene cyclase, terpenoid, X-ray crystallography Subject Categories Biochemistry | Chemistry This dissertation is available at ScholarlyCommons: https://repository.upenn.edu/edissertations/2181 STRUCTURAL AND FUNCTIONAL STUDIES OF TWO BACTERIAL TERPENE CYCLASES: GEOSMIN SYNTHASE AND EPI-ISOZIZAENE SYNTHASE Golda Harris Barrow A DISSERTATION in Chemistry Presented to the Faculties of the University of Pennsylvania in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy 2017 Supervisor of Dissertation ________________________ Dr. David W. Christianson Roy and Diana Vagelos Professor of Chemistry and Chemical Biology Graduate Group Chairperson ________________________ Dr. Gary A. Molander Hirschmann-Makineni Professor of Chemistry Dissertation Committee Dr. Ronen Marmorstein, Professor of Biochemistry and Biophysics Dr. E. James Petersson, Professor of Chemistry Dr. A. Joshua Wand, Benjamin Rush Professor of Biochemistry and Biophysics I dedicate this thesis to my parents, Philip and Helen Harris, for their love and support always. ii Acknowledgments During my time as a graduate student, I have had the opportunity to work with and learn from many wonderful scientists and people. First and foremost, this group includes my advisor, Dr. David Christianson. David has always encouraged me to learn as much as possible about science and to explore any research area that would help to answer our questions on enzyme function. He has been a kind and understanding mentor and a fantastic teacher. I am so grateful to have been a part of his lab during my time at Penn. I have also learned so much from many professors in the Chemistry and Biochemistry & Biophysics departments, from taking classes as a student and teaching others as a TA. In particular, I want to thank my dissertation committee, Dr. Ronen Marmorstein, Dr. James Petersson, and Dr. Josh Wand, for their scientific ideas and suggestions, encouragement to push outside my comfort zone, and kind mentorship over the years. My PhD work would have been impossible to finish without the help of my friends in the Chemistry department to get me through the past five years. I want to thank the cohort of biological chemistry graduate students who entered the program with me. Navigating our first year of graduate school classes and lab assignments was a process that we all helped each other through. I am fortunate to have had such a kind group of people with which to do so. Most importantly, I thank the members of the Christianson lab, past and present. In particular, I want to thank Dr. Ruiqiong Li, who welcomed me into the lab during my rotation project, and Dr. Christophe Decroos, who walked me through crystallographic refinement when I had no idea what I was doing. I thank Dr. Patrick Lombardi for laying iii the basis for my thesis work on geosmin synthase, and for his discussions for our paper on this project. I thank Dr. Travis Pemberton for teaching me so much about crystallography and SAXS, and for encouraging me out of my anti-social tendencies. I would most like to thank the current members of my lab: Dr. Travis Pemberton, Dr. Stephen Shinsky, Ben Roose (whom we borrow from the Dmochowski lab), Nick Porter, Patrick Blank, Jeremy Osko, and Jacque Faylo. Thank you for all of our laughs, and a few scientific discussions, over the years. Lastly, I want to thank my friends and family outside of the Penn community. To Lauren, my best friend in the whole wide world – thank you for always seeing the best in me, and reminding me how funny we are about seating choices. (We know chairs are the best.) To Aileen – thank you for your constant kindness and friendship, and for understanding when I need to vent about science or life in general. To my entire huge, extended family – thank you for always being the support system that I needed. I hope I can be the same for all of you. To my husband, Evan – thank you for your never-failing support, your love, and for reminding me to love myself, too. Thank you also for the laughter you bring to our home – and for all the kitten videos! To my parents, Philip and Helen – I am so grateful to be your daughter. Thank you for always supporting me in everything that I do, and providing so much help and love along the way. None of this work would be possible without you. I hope I continue to make you proud. iv ABSTRACT STRUCTURAL AND FUNCTIONAL STUDIES OF TWO BACTERIAL TERPENE CYCLASES: GEOSMIN SYNTHASE AND EPI-ISOZIZAENE SYNTHASE Golda Harris Barrow David W. Christianson Terpene cyclases convert acyclic isoprenoid precursors into complex cyclic terpenoid compounds. Hydrophobic active site contours in terpene cyclases direct cyclization reactions through a cascade of carbocation intermediates by serving as templates for terpenoid product structure. Both local molecular structure at the active site and global protein structure encompassing domain organization and oligomerization state have effects on catalytic function in terpene cyclases. The goal of this work is characterization of the effects of local structural changes to the active site of a terpene cyclase, and a thorough understanding of the structure-function relationship of active site structure and domain organization in two terpene cyclases, geosmin synthase (ScGS) and epi-isozizaene synthase (EIZS) from Streptomyces coelicolor. Geosmin synthase (ScGS) is a bifunctional class I sesquiterpene cyclase that catalyzes the conversion of FPP to germacradienol, germacrene D, and geosmin in unique cyclization and cyclization-fragmentation reactions occurring in separate active sites. We determined the X-ray crystal structure of the N-terminal domain of ScGS and homology models of the C-terminal domain of ScGS, and used small-angle X-ray scattering (SAXS) to propose models of domain association in this system. Product analysis by gas v chromatography-mass spectrometry (GC-MS) in this system indicates residues that are important for catalysis in the C-terminal domain cyclization-fragmentation reaction. EIZS is a promiscuous terpene cyclase