5GSN

Tmm in complex with methimazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 

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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:  
    5GSN, 5IPY, 5IQ1, 5IQ4

  • 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 is responsible for converting TMA to TMAO ...

    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

    Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Flavin-containing monooxygenaseA, B, C, D453Roseovarius nubinhibens ISMMutation(s): 3 
Gene Names: ISM_08155
UniProt
Find proteins for A3SLM3 (Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM))
Explore A3SLM3 
Go to UniProtKB:  A3SLM3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3SLM3
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.849α = 90
b = 207.578β = 90.31
c = 72.517γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
HKL-3000data processing
PHENIXphasing
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation of ChinaChina31290230

Revision History  (Full details and data files)

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