Semi-rational design of nitroarene dioxygenase for catalytic ability toward 2,4-dichloronitrobenzene

Journal article

Rieske non-heme dioxygenase family enzymes play an important role in the aerobic biodegradation of nitroaromatic pollutants, but no active dioxygenases are available in nature for initial reactions in the degradation of many refractory pollutants like 2,4-dichloronitrobenzene (24DCNB). Here, we report the engineering of hotspots in 2,3-dichloronitrobenzene dioxygenase from Diaphorobacter sp. strain JS3051, achieved through molecular dynamic simulation analysis and site-directed mutagenesis, with the aim of enhancing its catalytic activity toward 24DCNB. The computationally predicted activity scores were largely consistent with the detected activities in wet experiments. Among them, the two most beneficial mutations (E204M and M248I) were obtained, and the combined mutant reached up to a 62-fold increase in activity toward 24DCNB, generating a single product, 3,5-dichlorocatechol, which is a naturally occurring compound. In silico analysis confirmed that residue 204 affected the substrate preference for meta-substituted nitroarenes, while residue 248 may influence substrate preference by interaction with residue 295. Overall, this study provides a framework for manipulating nitroarene dioxygenases using computational methods to address various nitroarene contamination problems.

Authors: Xu, J; Li, T; Huang, WE; Zhou, N-Y

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: American Society for Microbiology
• Journal: Applied and Environmental Microbiology
• Volume: 90
• Issue: 6
• Article number: e01436-23
• Place of publication: United States
• Publication date: 2024-05-06
• Acceptance date: 2024-04-05
• DOI: 10.1128/aem.01436-23
• EISSN: 1098-5336
• ISSN: 0099-2240
• Pmid: 38709097
• Language: English
• Keywords: semi-rational design; site-directed mutagenesis; biodegradation; nitroarene dioxygenase; molecular dynamics simulation