PhD Studentship: Structure, function and application of prFMN dependent carboxylases

The University of Manchester - Academic School: School of Chemistry

Supervisors

Principal Supervisor: Professor David Leys

Anticipated start date for project: Available to start in April 2017, July 2017 or September 2017

Closing date for applications: open until position is filled

Summary of Project

The chemical repertoire of enzymes is greatly enhanced by cofactors: small inorganic or organic molecules that are bound by the protein matrix to constitute the active holo-enzyme. Our group has recently discovered a new type of cofactor: a prenylated-flavin that has azomethine ylide properties (Refs 1 and 2). This cofactor is an integral part of the widespread ubiD/ubiX system. The latter is implicated in the non-oxidative reversible decarboxylation of aromatic substrates, and plays a pivotal role in bacterial ubiquinone biosynthesis or microbial biodegradation of aromatic compounds. Our data strongly suggests 1,3-dipolar cycloaddition chemistry supports reversible decarboxylation in these enzymes, the first example of an enzymatic 1,3-dipolar cycloaddition reaction. Our model for UbiD catalysis hints at new routes in alkene hydrocarbon production or aryl (de)carboxylation.

The current application builds ambitiously on these results: we seek to investigate structure/function of relationships of the wider UbiD family, ultimately including the multi-subunit enzymes that couple ATP-hydrolysis to carboxylation. For many of these, the exact composition of the holo-enzyme has yet to be established, but a common feature is the fact multiple UbiD-like subunits form hetero-oligomers, often associated with smaller, distinct subunits. Given the lack of detailed structural information, it is unclear if and how coupling between ATP-hydrolysis or  substrate/product dephosphorylation and carboxylation is achieved. Our studies will be aimed at uncovering the molecular basis underpinning the coupling between ATP or phosphorylated substrate-hydrolysis and carboxylation. If we fail to crystallise the holo-enzyme, we will seek to crystallise the individual subunits and combine this approach with cryo-electron microscopy studies of the holo-enzyme. Our ultimate goal is to create ATP-driven carboxylases with appropriate substrate specificity, to apply in novel green routes to commodity chemicals.

A multidisciplinary approach is required to document enzyme mechanism to guide laboratory evolution experiments aimed at developing novel catalysts. This project seeks to use structural biology, advanced kinetics, analytical chemistry, spectroscopy and computational studies combined with state-of-the-art laboratory evolution studies to tackle the questions outlined above. The successful candidate will join the group of David Leys in the MIB (www.mib.ac.uk) working alongside other group members recruited on this ERC project.   

  1. Payne, K. A., et al,. (2015), Nature 522, 497-501
  2. White, M. D., et al. (2015), Nature 522, 502-506

Qualification

Applicants should have or expect a good II(i) honours degree (or an equivalent degree) in Chemistry or biochemistry.

Funding

This project is to be funded under the European Research Council (ERC) Programme. This Studentship is for 4 years covering tuition fees and a stipend of 14,296 for 2016/17. Eligibility restricted to UK/EU applicants.

Contact for further Information
For general admission information, please email: pg.chemistry@manchester.ac.uk.

Informal inquiries about the project should be sent to Prof. David Leys by email (David.Leys@manchester.ac.uk). Please note that to apply for this studentship you must submit the relevant information via the University’s online application form.

How to Apply

Complete an online application form using the following web link http://www.manchester.ac.uk/postgraduate/howtoapply/

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Type / Role:

PhD

Location(s):

Northern England