Substrate specificity of a branch of aromatic dioxygenases determined by three distinct motifs.

Autor: Cui C; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.; National Center of Technology Innovation for Synthetic Biology, Tianjin, China., Yang LJ; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.; National Center of Technology Innovation for Synthetic Biology, Tianjin, China., Liu ZW; State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, China., Shu X; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China., Zhang WW; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China., Gao Y; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China., Wang YX; State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, China., Wang T; State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, China., Chen CC; State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, China.; Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China., Guo RT; State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, China. guoreyting@hubu.edu.cn.; Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China. guoreyting@hubu.edu.cn., Gao SS; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. gaoss@tib.cas.cn.; National Center of Technology Innovation for Synthetic Biology, Tianjin, China. gaoss@tib.cas.cn.; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. gaoss@tib.cas.cn.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2024 Sep 03; Vol. 15 (1), pp. 7682. Date of Electronic Publication: 2024 Sep 03.
DOI: 10.1038/s41467-024-52101-2
Abstrakt: The inversion of substrate size specificity is an evolutionary roadblock for proteins. The Duf4243 dioxygenases GedK and BTG13 are known to catalyze the aromatic cleavage of bulky tricyclic hydroquinone. In this study, we discover a Duf4243 dioxygenase PaD that favors small monocyclic hydroquinones from the penicillic-acid biosynthetic pathway. Sequence alignments between PaD and GedK and BTG13 suggest PaD has three additional motifs, namely motifs 1-3, distributed at different positions in the protein sequence. X-ray crystal structures of PaD with the substrate at high resolution show motifs 1-3 determine three loops (loops 1-3). Most intriguing, loops 1-3 stack together at the top of the pocket, creating a lid-like tertiary structure with a narrow channel and a clearly constricted opening. This drastically changes the substrate specificity by determining the entry and binding of much smaller substrates. Further genome mining suggests Duf4243 dioxygenases with motifs 1-3 belong to an evolutionary branch that is extensively involved in the biosynthesis of natural products and has the ability to degrade diverse monocyclic hydroquinone pollutants. This study showcases how natural enzymes alter the substrate specificity fundamentally by incorporating new small motifs, with a fixed overall scaffold-architecture. It will also offer a theoretical foundation for the engineering of substrate specificity in enzymes and act as a guide for the identification of aromatic dioxygenases with distinct substrate specificities.
(© 2024. The Author(s).)
Databáze: MEDLINE
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