Structural and functional analysis of bacterial flavin-containing monooxygenase reveals its ping-pong-type reaction mechanism

Cho, Hyo Je; Cho, Ha Yeon; Kim, Kyung Jin; Kim, Myung Hee; Kim, Si Wouk; Kang, Beom Sik

doi:10.1016/j.jsb.2011.04.007

Cited by 30 publications

(48 citation statements)

References 27 publications

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“…The nitrogen-containing substrates interact with the isoalloxazine ring through Pi-cation interaction, while the sulfur-containing substrates form Pi-sulfur interactions with the isoalloxazine ring. In the case of methimazole binding to hFMO3, the molecular docking results presented in this work, with Pi-stacking interactions between this substrate and the FAD cofactor, are very similar to the crystallography data of the co-crystals of methimazole and yeast FMO (PDB ID: 2GVC) (Eswaramoorthy et al, 2006) and also indole/FAD interaction in the bacterial FMO (PDB ID:2XVJ) (Cho et al, 2011). The latter observation is in support of the suitability of the hFMO3 model for in silico molecular docking applications.…”

Section: Binding Mode Analysissupporting

confidence: 78%

Human flavin-containing monooxygenase 3: Structural mapping of gene polymorphisms and insights into molecular basis of drug binding

Gao

Catucci

Nardo

et al. 2016

Gene

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Human hepatic flavin-containing monooxygenase 3 (hFMO3) catalyses the monooxygenation of carbon-bound reactive heteroatoms and plays an important role in the metabolism of drugs and xenobiotics. Although numerous hFMO3 allelic variants have been identified in patients and their biochemical properties well-characterised in vitro, the molecular mechanisms underlying loss-offunction mutations have still not been elucidated due to lack of detailed structural information of hFMO3. Therefore, in this work a 3D structural model of hFMO3 was generated by homology modeling, evaluated by a variety of different bioinformatics tools, refined by molecular dynamics simulations and further assessed based on in vitro biochemical data. The molecular dynamics simulation results highlighted 4 flexible regions of the protein with some of them overlapping the data from trypsin digest. This was followed by structural mapping of 12 critical polymorphic variants and molecular docking experiments with five different known substrates/drugs of hFMO3 namely, benzydamine, sulindac sulphide, tozasertib, methimazole and trimethylamine. Localisation of these mutations on the hFMO3 model provided a structural explanation for their observed biological effects and docked models of hFMO3-drug complexes gave insights into their binding mechanis m demonstrating that nitrogen-and sulfur-containing substrates interact with the isoalloxazine ring through Pi-Cation interaction and Pi-Sulfur interactions, respectively. Finally, the data presented give insights into the drug binding mechanism of hFMO3 which could be valuable not only for screening of new chemical entities but more significantly for designing of novel inhibitors of this important Phase I drug metabolising enzyme.

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Section: Binding Mode Analysissupporting

confidence: 78%

Human flavin-containing monooxygenase 3: Structural mapping of gene polymorphisms and insights into molecular basis of drug binding

Gao

Catucci

Nardo

et al. 2016

Gene

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“…During the oxidative half‐reaction, some studies indicated that NADP + remains bound to Tmm (Alfieri et al ., ; Orru et al ., ). However, later structural analysis suggested that NADP + dissociates and the substrate binds before the oxidation (Cho et al ., ). Based on previous studies on indole and methimazole monooxygenation (Cho et al ., ; Beaty and Ballou, 1981a,b), it is reasonable to suppose that the catalysis of TMA by Tmm can be divided into a reductive half and a followed oxidative half (Fig.…”

Section: Introductionmentioning

confidence: 99%

Structural mechanism for bacterial oxidation of oceanic trimethylamine into trimethylamine N‐oxide

Chen

Zhang

et al. 2017

Molecular Microbiology

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SummaryTrimethylamine (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 1 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 1 undergoes a conformational change in the oxidative half-reaction of FMOs.

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“…FMO catalyzes the hydroxylation of indole to 2-hydroxyindole and 3-hydroxyindole by using the reducing power of NADPH in the presence of oxygen (Choi et al, 2003;Eaton and Chapman, 1995;Maugard et al, 2002). In the non-enzymatic reaction, indigo is produced from the combination of two 3-hydroxyindole molecules, whereas indirubin is made from the dimerization of 2-hydroxyindole and 3-hydroxyindole (Berry et al, 2002;Cho et al, 2011;Choi et al, 2003;Eaton and Chapman, 1995;Maugard et al, 2002;McClay et al, 2005). Currently, it is thought that the disproportional production of indigo and indirubin is due to random combinations of the various hydroxyindole molecules under different conditions, but any enzyme activity in the combination reaction has not been discovered yet.…”

Section: Introductionmentioning

confidence: 99%

Enhanced indirubin production in recombinant Escherichia coli harboring a flavin-containing monooxygenase gene by cysteine supplementation

Han

Gim

Kim

et al. 2013

Journal of Biotechnology

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Structural and functional analysis of bacterial flavin-containing monooxygenase reveals its ping-pong-type reaction mechanism

Cited by 30 publications

References 27 publications

Human flavin-containing monooxygenase 3: Structural mapping of gene polymorphisms and insights into molecular basis of drug binding

Human flavin-containing monooxygenase 3: Structural mapping of gene polymorphisms and insights into molecular basis of drug binding

Structural mechanism for bacterial oxidation of oceanic trimethylamine into trimethylamine N‐oxide

Enhanced indirubin production in recombinant Escherichia coli harboring a flavin-containing monooxygenase gene by cysteine supplementation

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