7D4N

Crystal structure of Tmm from strain HTCC7211 soaked with DMS for 20 min

Summary for 7D4N

• Entry DOI: 10.2210/pdb7d4n/pdb
• Descriptor: Flavin-containing monooxygenase FMO, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, FLAVIN-ADENINE DINUCLEOTIDE, ... (4 entities in total)
• Functional Keywords: trimethylamine monooxygenase, flavoprotein
• Biological source: Candidatus Pelagibacter sp. HTCC7211
• Total number of polymer chains: 2
• Total formula weight: 111316.32

Authors

Li, C.Y.,Zhang, Y.Z. (deposition date: 2020-09-24, release date: 2021-09-15, Last modification date: 2023-11-29)

Primary citation

Wang, X.J.,Zhang, N.,Teng, Z.J.,Wang, P.,Zhang, W.P.,Chen, X.L.,Zhang, Y.Z.,Chen, Y.,Fu, H.H.,Li, C.Y.
Structural and Mechanistic Insights Into Dimethylsulfoxide Formation Through Dimethylsulfide Oxidation.
Front Microbiol, 12:735793-735793, 2021

PubMed Abstract: Dimethylsulfide (DMS) and dimethylsulfoxide (DMSO) are widespread in marine environment, and are important participants in the global sulfur cycle. Microbiol oxidation of DMS to DMSO represents a major sink of DMS in marine surface waters. The SAR11 clade and the marine clade (MRC) are the most abundant heterotrophic bacteria in the ocean surface seawater. It has been reported that trimethylamine monooxygenase (Tmm, EC 1.14.13.148) from both MRC and SAR11 bacteria likely oxidizes DMS to generate DMSO. However, the structural basis of DMS oxidation has not been explained. Here, we characterized a Tmm homolog from the SAR11 bacterium sp. HTCC7211 (Tmm). Tmm exhibits DMS oxidation activity . We further solved the crystal structures of Tmm and Tmm soaked with DMS, and proposed the catalytic mechanism of Tmm, which comprises a reductive half-reaction and an oxidative half-reaction. FAD and NADPH molecules are essential for the catalysis of Tmm. In the reductive half-reaction, FAD is reduced by NADPH. In the oxidative half-reaction, the reduced FAD reacts with O to form the C4a-(hydro)peroxyflavin. The binding of DMS may repel the nicotinamide ring of NADP, and make NADP generate a conformational change, shutting off the substrate entrance and exposing the active C4a-(hydro)peroxyflavin to DMS to complete the oxidation of DMS. The proposed catalytic mechanism of Tmm may be widely adopted by MRC and SAR11 bacteria. This study provides important insight into the conversion of DMS into DMSO in marine bacteria, leading to a better understanding of the global sulfur cycle.

PubMed: 34630359
DOI: 10.3389/fmicb.2021.735793

Experimental method

X-RAY DIFFRACTION (1.999 Å)