Investigating terephthalate biodegradation: structural characterization of a putative decarboxylating cis-dihydrodiol dehydrogenase.
As a highly coveted precursor molecule, terephthalate (Tph) continues to be used extensively for the production of polyethylene Tph bottles, polyester films, and textile fibers worldwide. Based on its detrimental physiological effects, Tph is now recognized as a serious environmental pollutant. While amenable to biodegradation and, in fact, traditionally neutralized by aerobic microbiological processes, our current lack of understanding of the enzymatic degradation of Tph at the molecular level presents a major impediment in the development of robust bioremediation strategies. The biodegradation of Tph proceeds through a single metabolic intermediate (a cis-dihydrodiol), which is subsequently converted to the end product (protocatechuate) by a decarboxylating cis-dihydrodiol dehydrogenase (TphB). Using iodide single-wavelength anomalous dispersion, we report the first structural characterization of TphB to 1.85Å resolution. Contrary to prior speculations, a fluorescent scan unambiguously shows that TphB coordinates Zn(2+) and not Fe(2+). The molecular architecture of TphB provides a rationale to the primary-level divergence observed between TphB and other cis-dihydrodiol dehydrogenases while explaining its intriguingly close evolutionary clustering with non-dihydrodiol dehydrogenases belonging to the isocitrate/isopropylmalate family of enzymes. Sequence and structural analyses reveal a putative substrate-binding pocket proximal to the bound Zn(2+). In silico substrate modeling in this putative binding pocket suggests a mechanistic sequence relying on H291, K295, and Zn(2+) as core mediators of catalytic turnover. Overall, this study reveals novel structural and mechanistic insights into a decarboxylating cis-dihydrodiol dehydrogenase that mediates one of the two catalytic steps in the biodegradation of the environmental pollutant Tph.
Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 3P6.
Jasleen
J
Bains
Jeremy E
JE
Wulff
Martin J
MJ
Boulanger
D001673:Biodegradation, Environmental; D019117:Burkholderia / Q000737:chemistry / Q000201:enzymology*; D002384:Catalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D003653:Decarboxylation; D004785:Environmental Pollutants / Q000378:metabolism*; D007501:Iron / Q000378:metabolism; D007700:Kinetics; D010088:Oxidoreductases / Q000737:chemistry* / Q000378:metabolism; D010795:Phthalic Acids / Q000737:chemistry* / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D013379:Substrate Specificity; D015032:Zinc / Q000378:metabolism
D004785:Environmental Pollutants; D010795:Phthalic Acids; C011363:terephthalic acid; D007501:Iron; D010088:Oxidoreductases; C048338:trans-1,2-dihydrobenzene-1,2-diol dehydrogenase; D015032:Zinc