5GSN

Tmm in complex with methimazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.203 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

Li, C.Y.Chen, X.L.Zhang, D.Wang, P.Sheng, Q.Peng, M.Xie, B.B.Qin, Q.L.Li, P.Y.Zhang, X.Y.Su, H.N.Song, X.Y.Shi, M.Zhou, B.C.Xun, L.Y.Chen, Y.Zhang, Y.Z.

(2017) Mol. Microbiol. 103: 992-1003

  • DOI: 10.1111/mmi.13605
  • Primary Citation of Related Structures:  

  • PubMed 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 ...

    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.


    Organizational Affiliation

    State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan, 250100, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Flavin-containing monooxygenase
A, B, C, D
453Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM)Mutation(s): 3 
Find proteins for A3SLM3 (Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM))
Go to UniProtKB:  A3SLM3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MMZ
Query on MMZ

Download SDF File 
Download CCD File 
A, C
1-METHYL-1,3-DIHYDRO-2H-IMIDAZOLE-2-THIONE
METHIMAZOLE
C4 H6 N2 S
PMRYVIKBURPHAH-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B, C, D
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.203 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.849α = 90.00
b = 207.578β = 90.31
c = 72.517γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data processing
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-08-16 
  • Released Date: 2017-01-18 
  • Deposition Author(s): Zhang, Y.Z., Li, C.Y.

Funding OrganizationLocationGrant Number
National Science Foundation of ChinaChina31290230

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-03-22
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Data collection