6LR1

Hexachlorobenzene Monooxygenase (HcbA1) from Nocardioides sp. strain PD653

Summary for 6LR1

• Entry DOI: 10.2210/pdb6lr1/pdb
• Descriptor: Hexachlorobenzene oxidative dehalogenase (2 entities in total)
• Functional Keywords: hexachlorobenzene, flavin dependent two-component monooxygenase, dechlorinase, oxidoreductase
• Biological source: Nocardioides sp. PD653
• Total number of polymer chains: 2
• Total formula weight: 100384.66

Authors

Guo, Y.,Zheng, J.T.,Zhou, N.Y. (deposition date: 2020-01-15, release date: 2020-01-29, Last modification date: 2023-11-29)

Primary citation

Guo, Y.,Li, D.F.,Ji, H.,Zheng, J.,Zhou, N.Y.
Hexachlorobenzene Monooxygenase Substrate Selectivity and Catalysis: Structural and Biochemical Insights.
Appl.Environ.Microbiol., 87:-, 2020

PubMed Abstract: Hexachlorobenzene (HCB), as one of the persistent organic pollutants (POPs) and a possible human carcinogen, is especially resistant to biodegradation. In this study, HcbA1A3, a distinct flavin-N5-peroxide-utilizing enzyme and the sole known naturally occurring aerobic HCB dechlorinase, was biochemically characterized. Its apparent preference for HCB in binding affinity revealed that HcbA1 could oxidize only HCB rather than less-chlorinated benzenes such as pentachlorobenzene and tetrachlorobenzenes. In addition, the crystal structure of HcbA1 and its complex with flavin mononucleotide (FMN) were resolved, revealing HcbA1 to be a new member of the bacterial luciferase-like family. A much smaller substrate-binding pocket of HcbA1 than is seen with its close homologues suggests a requirement of limited space for catalysis. In the active center, Tyr362 and Asp315 are necessary in maintaining the normal conformation of HcbA1, while Arg311, Arg314, Phe10, Val59, and Met12 are pivotal for the substrate affinity. They are supposed to place HCB at a productive orientation through multiple interactions. His17, with its close contact with the site of oxidation of HCB, probably fixes the target chlorine atom and stabilizes reaction intermediates. The enzymatic characteristics and crystal structures reported here provide new insights into the substrate specificity and catalytic mechanism of HcbA1, which paves the way for its rational engineering and application in the bioremediation of HCB-polluted environments. As an endocrine disrupter and possible carcinogen to human beings, hexachlorobenzene (HCB) is especially resistant to biodegradation, largely due to difficulty in its dechlorination. The lack of knowledge of HCB dechlorinases limits their application in bioremediation. Recently, an HCB monooxygenase, HcbA1A3, representing the only naturally occurring aerobic HCB dechlorinase known so far, was reported. Here, we report its biochemical and structural characterization, providing new insights into its substrate selectivity and catalytic mechanism. This research also increases our understanding of HCB dechlorinases and flavin-N5-peroxide-utilizing enzymes.

PubMed: 33097503
DOI: 10.1128/AEM.01965-20

Experimental method

X-RAY DIFFRACTION (2.5 Å)