Characterizing Protocatechuate Dioxygenase Superfamily Members: DesB Inhibition and Allosterism

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The reality of global climate change and strain on fossil fuel reserves make the need for sustainable sources of fuel increasingly urgent. Second generation biofuels produced from lignocellulosic biomass offers a sustainable and efficient alternative resource for energy. With over 200 billion tons of lignin being produced as waste by the paper production industry, lignin is an untapped resource. A bacterium called Sphingobium sp. SYK-6 has the ability to degrade lignin using three dioxygenases from the Protocatechuate Dioxygenase Superfamily, LigAB, DesB, and DesZ. These dioxygenases are essential to the metabolism of lignin because they can cleave certain lignin derived aromatic compounds which allows their conversion into the metabolites necessary for entrance into the TCA cycle. DesB and LigAB were found to have a 30% sequence similarity, with nearly identical active site residues and Fe (II) centers. However, while LigAB is substrate promiscuous, being able to catalyze the ring opening for several compounds, DesB exhibits strict substrate specificity, only catalyzing the ring opening of its natural substrate, gallate. Furthermore, previous studies in the Taylor Lab demonstrated that DesB was inhibited by several lignin-derived compounds. This project explored the extent of DesB's inhibition with these compounds through Ki determination. Moreover, DesB was thought to have an allosteric site that was analogous to the known allosteric site of LigAB. Additional kinetic studies with PCA, the strongest inhibitor of DesB, syringate, and vanillin, showed that these inhibitors exhibited mixed inhibition. It is possible that the putative allosteric site in DesB could influence the nature of inhibition of these compounds. Future studies will explore this allosteric site through mutagenesis and kinetic assays.

    Item Description
    Name(s)
    Thesis advisor: Taylor, Erika A.
    Date
    April 15, 2017
    Extent
    55 pages
    Language
    eng
    Genre
    Physical Form
    electronic
    Discipline
    Rights and Use
    In Copyright – Non-Commercial Use Permitted
    Restrictions on Use
    Access restricted until April 15, 2023. Please contact wesscholar@wesleyan.edu for more information.
    Digital Collection
    PID
    ir:1877