A protein used by common soil bacteria is providing new clues in the effort to convert aryl compounds, a common waste product from industrial and agricultural practices, into something of value. The protein structure of the enzyme LigM was determined using X-ray crystallography, revealing novel structural elements (red in figure) and a conserved tetrahydrofolate-binding domain (gray), with LigM binding to its substrates (green) using internal binding cavities.
Researchers used have resolved the soil bacterium Sphingomonas to metabolize aryl compounds derived from lignin, the stiff, organic material that gives plants their structure. In biofuel production, aryl compounds are a byproduct of the breakdown of lignin, some pathways of which involve demethylation, an often critical precursor to additional modification steps of lignin-derived aryl compounds. The simple, single-enzyme system of LigM, as well as its functionality over a broad temperature range, makes it an attractive demethylase for use in aromatic conversion. Other findings included: half the LigM enzyme was homologous to known structures with a tetrahydrofolate-binding domain that is found in both simple and complex organisms; the other half of LigM’s structure is completely unique, providing a starting point for determining where its aryl substrate-binding site is located; and LigM is a tyrosine-dependent demethylase. This research provides groundwork needed to aid in developing an enzyme-based system for converting aromatic waste into useful products.
Kohlera, A. C., et al. “Structure of Aryl O-Demethylase Offers Molecular Insight into a Catalytic Tyrosine-Dependent Mechanism.” PNAS 114(16), E3205–E3214 (2017). [DOI:10.1073/pnas.1619263114].
Instruments and Facilities Used: Beam line 8.2.2 and X-ray macromolecular crystallography at Berkeley Center for Structural Biology Advanced Light Source at Lawrence Berkeley National Laboratory.
Funding Acknowledgements: Crystallographic work: Berkeley Center for Structural Biology (BCSB) Advanced Light Source (ALS) beam line 8.2.2. BCSB ALS staff: technical support; J. H. Pereira: assistance in early stages of crystallographic work. BCSB support in part: National Institutes of Health’s (NIH) National Institute of General Medical Sciences (NIGMS) and Howard Hughes Medical Institute (HHMI). ALS support: Office of Basic Energy Sciences (OBES), Director, U.S. Department of Energy (DOE) Office of Science, under Contract DE-AC02-05CH11231. Work conducted by Joint BioEnergy Institute (JBEI) and supported by Office of Biological and Environmental Research (OBER), DOE Office of Science, under Contract DE-AC02-05CH11231.