Building chemical tools from the indolmycin biosynthetic pathway
department or school: Science, Faculty of
department or school: Chemistry, Department of
data provider: DSpace
degree campus: UBCV
creator: Hoffarth, Elesha Rene
issued: 2022-04-30T07:00:00Z
issued: 2021
related degree: Doctor of Philosophy - PhD
degree grantor: University of British Columbia
description: Natural products are essential to the discovery of new drugs, including antibiotics. Industrial interest in natural products has declined since the 1980s, but advances in biocatalysis and biosynthetic knowledge have helped revive interest in natural products as these advances contribute to more feasible discovery, production and derivatization of natural products. To continue this industrial interest in natural products and their related compounds, work should be done to accumulate more biosynthetic knowledge to further improve methods of discovery, production and derivatization and facilitate more widespread use of biocatalysts. Indolmycin is a natural product with antibiotic activities against methicillin-resistant Staphylococcus aureus, Helicobacter pylori and Plasmodium falciparum, whose biosynthetic pathway is shown here to be a source of new biochemical tools. First, in order to better understand the unique reactivity of the rare oxygen- and pyridoxal 5′-phosphate (PLP)-dependent arginine desaturases discovered from the indolmycin biosynthetic pathway, the first X-ray crystal structure of an arginine desaturase was solved. This structure showed an active site that was highly similar to the related oxygen- and PLP-dependent hydroxylases. Catalytic residues for the arginine desaturases were uncovered by creating mutagenic variants based on the crystal structure information. Second, sequence similarity analysis and side-product analysis were done, which further supported a higher similarity to the arginine hydroxylases than was originally predicted. Additionally, superoxide was shown to be an intermediate of the arginine oxidase mechanism for the first time through EPR and cytochrome c assays. Based on this information, a unified mechanistic hypothesis is proposed which suggests that desaturation and hydroxylation may be differentiated by the presence/position of water in the active site. Third, the indolmycin biosynthetic enzymes are used in conjunction with a p…
aggregated CHO: https://circle.library.ubc.ca/rest/handle/2429/77771
note: BUILDING CHEMICAL TOOLS FROM THE INDOLMYCIN BIOSYNTHETIC PATHWAY by ELESHA RENE HOFFARTH B.Sc., The University of Calgary, 2014 A DISSERTATION SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Chemistry) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) April 2021 © Elesha Rene Hoffarth, 2021 ii The following individuals certify that they have read, and recommend to the Faculty of Graduate and Postdoctoral Studies for acceptance, the dissertation entitled: Building chemical tools from the indolmycin biosynthetic pathway. submitted by Elesha Rene Hoffarth in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemistry Examining Committee: Dr. Katherine S. Ryan, Associate Professor, Chemistry, University of British Columbia Supervisor Dr. Stephen G. Withers, Professor, Chemistry, University of British Columbia Supervisory Committee Member Dr. Laurel L. Schafer, Professor, Chemistry, University of British Columbia University Examiner Dr. Natalie Strynadka, Professor, Biochemistry and Molecular Biology, University of British Columbia University Examiner Dr. Erika Plettner, Professor, Chemistry, Simon Fraser University External Examiner Additional Supervisory Committee Members: Dr. Mark MacLachlan, Professor, Chemistry, University of British Columbia Supervisory Committee Member Dr. Martin Tanner, Professor, Chemistry, University of British Columbia Supervisory Committee Member iii Abstract Natural products are essential to the discovery of new drugs, including antibiotics. Industrial interest in natural products has declined since the 1980s, but advances in biocatalysis and biosynthetic knowledge have helped revive interest in natural products as these advances contribute to more feasible discovery, production and derivatization of natural products. To continue this industrial interest in natural products and their related compounds, work should be …
has type: Thesis/Dissertation
date issued: 2021-05
is shown at: 10.14288/1.0396679
language: eng
degree discipline: Chemistry
provider: Vancouver : University of British Columbia Library
publisher: University of British Columbia
rights: Attribution-NonCommercial-NoDerivatives 4.0 International
rights URI: http://creativecommons.org/licenses/by-nc-nd/4.0/
scholar level: Graduate
type: Text
identifier URI: http://hdl.handle.net/2429/77771