4ATY

Crystal structure of a Terephthalate 1,2-cis-dihydrodioldehydrogenase from Burkholderia xenovorans LB400

Summary for 4ATY

• Entry DOI: 10.2210/pdb4aty/pdb
• Descriptor: TEREPHTHALATE 1,2-CIS-DIHYDRODIOL DEHYDROGENASE, ZINC ION, BETA-MERCAPTOETHANOL, ... (4 entities in total)
• Functional Keywords: oxidoreductase
• Biological source: BURKHOLDERIA XENOVORANS LB400
• Total number of polymer chains: 1
• Total formula weight: 36489.17

Authors

Bains, J.,Boulanger, M.J. (deposition date: 2012-05-11, release date: 2012-08-22, Last modification date: 2024-05-08)

Primary citation

Bains, J.,Wulff, J.E.,Boulanger, M.J.
Investigating Terephthalate Biodegradation: Structural Characterization of a Putative Decarboxylating Cis-Dihydrodiol Dehydrogenase.
J.Mol.Biol., 423:284-, 2012

PubMed Abstract: 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.

PubMed: 22889862
DOI: 10.1016/J.JMB.2012.07.022

Experimental method

X-RAY DIFFRACTION (1.85 Å)