title: Structural mechanism for bacterial oxidation of oceanic trimethylamine into trimethylamine N-oxide.
abstract: Trimethylamine (TMA) and trimethylamine N-oxide (TMAO) are widespread in the ocean and are important nitrogen source for bacteria. TMA monooxygenase (Tmm), a bacterial flavin-containing monooxygenase (FMO), is found widespread in marine bacteria and is responsible for converting TMA to TMAO. However, the molecular mechanism of TMA oxygenation by Tmm has not been explained. Here, we determined the crystal structures of two reaction intermediates of a marine bacterial Tmm (RnTmm) and elucidated the catalytic mechanism of TMA oxidation by RnTmm. The catalytic process of Tmm consists of a reductive half-reaction and an oxidative half-reaction. In the reductive half-reaction, FAD is reduced and a C4a-hydroperoxyflavin intermediate forms. In the oxidative half-reaction, this intermediate attracts TMA through electronic interactions. After TMA binding, NADP+bends and interacts with D317, shutting off the entrance to create a protected micro-environment for catalysis and exposing C4a-hydroperoxyflavin to TMA for oxidation. Sequence analysis suggests that the proposed catalytic mechanism is common for bacterial Tmms. These findings reveal the catalytic process of TMA oxidation by marine bacterial Tmm and first show that NADP+undergoes a conformational change in the oxidative half-reaction of FMOs.
authors.affiliation: State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.
authors.forename: Chun-Yang
authors.initials: CY
authors.lastname: Li
authors.affiliation: State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.
authors.forename: Xiu-Lan
authors.initials: XL
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.
authors.forename: Dian
authors.initials: D
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Sheng
authors.affiliation: State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Peng
authors.affiliation: State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.
authors.forename: Bin-Bin
authors.initials: BB
authors.lastname: Xie
authors.affiliation: State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.
authors.forename: Qi-Long
authors.initials: QL
authors.lastname: Qin
authors.affiliation: State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.
authors.forename: Ping-Yi
authors.initials: PY
authors.lastname: Li
authors.affiliation: State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.
authors.forename: Xi-Ying
authors.initials: XY
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.
authors.forename: Hai-Nan
authors.initials: HN
authors.lastname: Su
authors.affiliation: State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.
authors.forename: Xiao-Yan
authors.initials: XY
authors.lastname: Song
authors.affiliation: State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.
authors.forename: Mei
authors.initials: M
authors.lastname: Shi
authors.affiliation: State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.
authors.forename: Bai-Cheng
authors.initials: BC
authors.lastname: Zhou
authors.affiliation: State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.
authors.forename: Lu-Ying
authors.initials: LY
authors.lastname: Xun
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
authors.forename: Yin
authors.initials: Y
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.|Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
authors.forename: Yu-Zhong
authors.initials: YZ
authors.lastname: Zhang
mesh_terms: D000595:Amino Acid Sequence; D057486:Carbon Cycle / Q000502:physiology; D002384:Catalysis; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D005415:Flavins / Q000378:metabolism; D008744:Methylamines / Q000378:metabolism*; D009249:NADP / Q000378:metabolism*; D058458:Nitrogen Cycle / Q000502:physiology; D010084:Oxidation-Reduction; D010105:Oxygenases / Q000235:genetics / Q000378:metabolism* / Q000648:ultrastructure; D020836:Protein Structure, Quaternary; D041902:Rhodobacteraceae / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D016415:Sequence Alignment
chemical_list: C531259:C4a-hydroperoxyflavin; D005415:Flavins; D008744:Methylamines; D009249:NADP; D010105:Oxygenases; C043996:tertiary amine monooxygenase; C005855:trimethyloxamine; C023336:trimethylamine