1TMO

TRIMETHYLAMINE N-OXIDE REDUCTASE FROM SHEWANELLA MASSILIA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of oxidized trimethylamine N-oxide reductase from Shewanella massilia at 2.5 A resolution.

Czjzek, M.Dos Santos, J.P.Pommier, J.Giordano, G.Mejean, V.Haser, R.

(1998) J Mol Biol 284: 435-447

  • DOI: 10.1006/jmbi.1998.2156
  • Primary Citation of Related Structures:  
    1TMO

  • PubMed Abstract: 
  • The periplasmic trimethylamine N-oxide (TMAO) reductase from the marine bacteria Shewanella massilia is involved in a respiratory chain, having trimethylamine N-oxide as terminal electron acceptor. This molybdoenzyme belongs to the dimethyl sulfoxide ...

    The periplasmic trimethylamine N-oxide (TMAO) reductase from the marine bacteria Shewanella massilia is involved in a respiratory chain, having trimethylamine N-oxide as terminal electron acceptor. This molybdoenzyme belongs to the dimethyl sulfoxide (DMSO) reductase family, but has a different substrate specificity than its homologous enzyme. While the DMSO reductases reduce a broad spectra of organic S-oxide and N-oxide compounds, TMAO reductase from Shewanella massilia reduces only TMAO as the natural compound. The crystal structure was solved by molecular replacement with the coordinates of the DMSO reductase from Rhodobacter sphaeroides. The overall fold of the protein structure is essentially the same as the DMSO reductase structures, organized into four domains. The molybdenum coordination sphere is closest to that described in the DMSO reductase of Rhodobacter capsulatus. The structural differences found in the protein environment of the active site could be related to the differences in substrate specificity of these enzymes. In close vicinity of the molybdenum ion a tyrosine residue is missing in the TMAO reductase, leaving a greater space accessible to the solvent. This tyrosine residue has contacts to the oxo groups in the DMSO reductase structures. The arrangement and number of charged residues lining the inner surface of the funnel-like entrance to the active site, is different in the TMAO reductase than in the DMSO reductases from Rhodobacter species. Furthermore a surface loop at the top of the active-site funnel, for which no density was present in the DMSO reductase structures, is well defined in the oxidized form of the TMAO reductase structure, and is located on the border of the funnel-like entrance of the active center.


    Related Citations: 
    • Molecular Analysis of the Trimethylamine N-Oxide (Tmao) Reductase Respiratory System from a Shewanella Species
      Dos Santos, J.P., Iobbi-Nivol, C., Couillault, C., Giordano, G., Mejean, V.
      (1998) J Mol Biol 284: 421

    Organizational Affiliation

    Laboratoire d'Architecture et Fonction de Macromolécules Biologiques, AFMB-CNRS Marseille, IBSM, 31 chemin Joseph Aiguier, Marseille Cedex 20, 13402, France. czjzek@afmb.cnrs-mrs.fr



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRIMETHYLAMINE N-OXIDE REDUCTASEA829Shewanella massiliaMutation(s): 0 
Gene Names: torA
EC: 1.6.6.9 (PDB Primary Data), 1.7.2.3 (UniProt)
Find proteins for O87948 (Shewanella massilia)
Explore O87948 
Go to UniProtKB:  O87948
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2MD
Query on 2MD

Download CCD File 
A
GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL) ESTER
C20 H28 N10 O13 P2 S2
YDYCAANTTOPADF-JKOCJXFLSA-N
 Ligand Interaction
2MO
Query on 2MO

Download CCD File 
A
MOLYBDENUM (IV)OXIDE
Mo O2
QXYJCZRRLLQGCR-OMUOWVJPAU
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.32α = 90
b = 140.7β = 90
c = 59.39γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-03-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance