Binding interaction of a ring-hydroxylating dioxygenase with fluoranthene in Pseudomonas aeruginosa DN1

• Published in: Scientific reports Vol. 11; no. 1; pp. 21317 - 11
• Main Authors: Xue, Shu-Wen, Tian, Yue-Xin, Pan, Jin-Cheng, Liu, Ya-Ni, Ma, Yan-Ling
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 29.10.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 631/326; 631/535; 704/172; Amino Acid Sequence; Amino acids; Bacterial Proteins - chemistry; Biodegradation; Carbon sources; Catalysis; Crystal structure; Dioxygenase; Dioxygenases - genetics; Dioxygenases - metabolism; Enzymes; Fluoranthene; Fluorenes - chemistry; Fluorenes - metabolism; Gene Knockout Techniques; Genes; Genetic engineering; Homology; Humanities and Social Sciences; Laboratories; Life sciences; Molecular Docking Simulation; Molecular weight; multidisciplinary; Mutagenesis, Site-Directed; Oxidation; Pseudomonas aeruginosa; Pseudomonas aeruginosa - enzymology; Pseudomonas aeruginosa - genetics; Pseudomonas aeruginosa - metabolism; Science; Science (multidisciplinary); Site-directed mutagenesis
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-021-00783-9

Pseudomonas aeruginosa DN1 can efficiently utilize fluoranthene as its sole carbon source, and the initial reaction in the biodegradation process is catalyzed by a ring-hydroxylating dioxygenase (RHD). To clarify the binding interaction of RHD with fluoranthene in the strain DN1, the genes encoding alpha subunit (RS30940) and beta subunit (RS05115) of RHD were functionally characterized through multi-technique combination such as gene knockout and homology modeling as well as molecular docking analysis. The results showed that the mutants lacking the characteristic alpha subunit and/or beta subunit failed to degrade fluoranthene effectively. Based on the translated protein sequence and Ramachandran plot, 96.5% of the primary amino-acid sequences of the alpha subunit in the modeled structure of the RHD were in the permitted region, 2.3% in the allowed region, but 1.2% in the disallowed area. The catalytic mechanism mediated by key residues was proposed by the simulations of molecular docking, wherein the active site of alpha subunit constituted a triangle structure of the mononuclear iron atom and the two oxygen atoms coupled with the predicted catalytic ternary of His 217 -His 222 -Asp 372 for the dihydroxylation reaction with fluoranthene. Those amino acid residues adjacent to fluoranthene were nonpolar groups, and the C 7 -C 8 positions on the fluoranthene ring were estimated to be the best oxidation sites. The distance of C 7 -O and C 8 -O was 3.77 Å and 3.04 Å respectively, and both of them were parallel. The results of synchronous fluorescence and site-directed mutagenesis confirmed the roles of the predicted residues during catalysis. This binding interaction could enhance our understanding of the catalytic mechanism of RHDs and provide a solid foundation for further enzymatic modification.