Post-translational modifications as a route to new chemistry, useful enzymes, and unexpected mechanisms

Nguyen, Dinh Thanh

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https://hdl.handle.net/2142/127491 Copy

Description

Title

Post-translational modifications as a route to new chemistry, useful enzymes, and unexpected mechanisms

Author(s)

Nguyen, Dinh Thanh

Issue Date

2024-12-05

Director of Research (if dissertation) or Advisor (if thesis)

• van der Donk, Wilfred Adrianus
• Mitchell, Douglas Alan

Doctoral Committee Chair(s)

• van der Donk, Wilfred Adrianus
• Mitchell, Douglas Alan

Committee Member(s)

• Nair, Satish K
• Chan, Jefferson Kar Fai

Department of Study

Chemistry

Discipline

Chemistry

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• Enzymes
• Natural Products

Abstract

Advances in directed evolution, which tailored enzymes to catalyze reactions on the substrate(s) of interest, facilitated the development of biocatalytic routes toward therapeutics. Additionally, enzymes catalyze remarkable transformations to construct privileged scaffolds that benefit drug discovery campaigns. The mentioned drug discovery and development efforts often rely on available reported enzymatic transformations, underscoring the need to discover new enzyme chemistry and enzymes with broad substrate tolerance. A common challenge in this pursuit is identifying the correct substrate(s) of uncharacterized enzymes of interest. This obstacle can be circumvented when exploring enzymes involved in ribosomally-synthesized and post-translationally modified peptides (RiPPs), as their substrates are genomically encoded peptides. In Chapter 1, I review advances in mining genomes for novel RiPP enzymes and briefly describe how they influence my thesis research. In Chapter 2, I describe the discovery of aminopyruvatides, a novel class of cyclic RiPPs biosynthesized by three distinct metalloenzymes. This work highlights a novel enzyme catalyzing the unprecedented conversion of C-terminal aspartate to aminopyruvate and the detailed structural characterization with multiple state-of-the-art techniques, including microcrystal electron diffraction. Chapter 3 describes how the substrate information and the genomic context guided me to discover that the [4+2] cyclase in Micromonospora rosaria is a substrate-tolerant enzyme, producing 14- to 68-membered pyridine-based cyclic peptides with diverse sequences. In Chapter 4, I investigate the substrate recognition mechanism of a tRNA-dependent enzyme previously discovered in the van der Donk lab through genome mining. This investigation revealed the role of a cryptic coiled-coil domain in recognizing the anticodon of tRNAs. Collectively, I demonstrate that uncharacterized RiPP pathways are a rich reservoir of novel chemistry, useful enzymes, and unexpected mechanisms.

Graduation Semester

2024-12

Type of Resource

Thesis

Handle URL

https://hdl.handle.net/2142/127491

Copyright and License Information

Copyright 2024 Dinh Nguyen

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