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PDBsum entry 1tmo

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Oxidoreductase PDB id
1tmo
Jmol
Contents
Protein chain
794 a.a. *
Ligands
2MD-2MD-2MO
Waters ×505
* Residue conservation analysis
PDB id:
1tmo
Name: Oxidoreductase
Title: Trimethylamine n-oxide reductase from shewanella massilia
Structure: Trimethylamine n-oxide reductase. Chain: a. Synonym: tmao reductase. Ec: 1.6.6.9
Source: Shewanella massilia. Organism_taxid: 76854. Cellular_location: periplasm. Other_details: marine bacteria, isolated from the fish mullus surmuletus
Resolution:
2.50Å     R-factor:   0.182     R-free:   0.247
Authors: M.Czjzek,J.P.Dos Santos,G.Giordano,V.Mejean
Key ref:
M.Czjzek et al. (1998). Crystal structure of oxidized trimethylamine N-oxide reductase from Shewanella massilia at 2.5 A resolution. J Mol Biol, 284, 435-447. PubMed id: 9813128 DOI: 10.1006/jmbi.1998.2156
Date:
03-Aug-98     Release date:   30-Mar-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O87948  (TORA_SHEMA) -  Trimethylamine-N-oxide reductase
Seq:
Struc:
 
Seq:
Struc:
829 a.a.
794 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.7.2.3  - Trimethylamine-N-oxide reductase (cytochrome c).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Trimethylamine + 2 (ferricytochrome c)-subunit + H2O = trimethylamine N-oxide + 2 (ferrocytochrome c)-subunit + 2 H+
Trimethylamine
+ 2 × (ferricytochrome c)-subunit
+ H(2)O
= trimethylamine N-oxide
+ 2 × (ferrocytochrome c)-subunit
+ 2 × H(+)
      Cofactor: Bis(molybdopterin guanine dinucleotide)molybdenum
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   1 term 
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     electron carrier activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1006/jmbi.1998.2156 J Mol Biol 284:435-447 (1998)
PubMed id: 9813128  
 
 
Crystal structure of oxidized trimethylamine N-oxide reductase from Shewanella massilia at 2.5 A resolution.
M.Czjzek, J.P.Dos Santos, J.Pommier, G.Giordano, V.Méjean, R.Haser.
 
  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 (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.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. The two amino acid stretches from 100 to 118 and 142 to 149 contain the residues involved in the coordination of the molybdenum ion and the oxo-groups. One can clearly see, that the conformation of the main-chain in the TMAO reductase (atom-type colors) has changed with respect to that of the DMSO reductases from Rhodobacter sphaeroides (light blue) or Rhodobacter capsulatus (dark blue), especially at the position 116 which corresponds to the Tyr114 in the DMSO reductases.
Figure 5.
Figure 5. Coordination sphere of the molybdenum ion MoVI as observed in the oxidized TMAO reductase of Shewanella massilia. The molybdenum (brown) is ligated by four sulfur atoms (green), two oxo groups (red) and the Og of Ser149. O1 is hydrogen bonded to a water molecule and O2 is hydrogen bonded to N epsilon 1 of Trp118.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 284, 435-447) copyright 1998.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19959582 P.J.Simpson, D.J.Richardson, and R.Codd (2010).
The periplasmic nitrate reductase in Shewanella: the resolution, distribution and functional implications of two NAP isoforms, NapEDABC and NapDAGHB.
  Microbiology, 156, 302-312.  
19452052 M.J.Romão (2009).
Molybdenum and tungsten enzymes: a crystallographic and mechanistic overview.
  Dalton Trans, (), 4053-4068.  
18522945 O.Genest, M.Neumann, F.Seduk, W.Stöcklein, V.Méjean, S.Leimkühler, and C.Iobbi-Nivol (2008).
Dedicated metallochaperone connects apoenzyme and molybdenum cofactor biosynthesis components.
  J Biol Chem, 283, 21433-21440.  
18175314 Y.Qiu, R.Zhang, T.A.Binkowski, V.Tereshko, A.Joachimiak, and A.Kossiakoff (2008).
The 1.38 A crystal structure of DmsD protein from Salmonella typhimurium, a proofreading chaperone on the Tat pathway.
  Proteins, 71, 525-533.
PDB code: 1s9u
17130127 B.J.Jepson, S.Mohan, T.A.Clarke, A.J.Gates, J.A.Cole, C.S.Butler, J.N.Butt, A.M.Hemmings, and D.J.Richardson (2007).
Spectropotentiometric and structural analysis of the periplasmic nitrate reductase from Escherichia coli.
  J Biol Chem, 282, 6425-6437.
PDB code: 2nya
18021072 E.V.Morozkina, and R.A.Zvyagilskaya (2007).
Nitrate reductases: structure, functions, and effect of stress factors.
  Biochemistry (Mosc), 72, 1151-1160.  
16286471 A.Vergnes, J.Pommier, R.Toci, F.Blasco, G.Giordano, and A.Magalon (2006).
NarJ chaperone binds on two distinct sites of the aponitrate reductase of Escherichia coli to coordinate molybdenum cofactor insertion and assembly.
  J Biol Chem, 281, 2170-2176.  
16962969 D.P.Kloer, C.Hagel, J.Heider, and G.E.Schulz (2006).
Crystal structure of ethylbenzene dehydrogenase from Aromatoleum aromaticum.
  Structure, 14, 1377-1388.
PDB code: 2ivf
15786505 A.J.Millar, C.J.Doonan, P.D.Smith, V.N.Nemykin, P.Basu, and C.G.Young (2005).
Oxygen atom transfer in models for molybdenum enzymes: isolation and structural, spectroscopic, and computational studies of intermediates in oxygen atom transfer from molybdenum(VI) to phosphorus(III).
  Chemistry, 11, 3255-3267.  
15716436 J.A.Müller, and S.DasSarma (2005).
Genomic analysis of anaerobic respiration in the archaeon Halobacterium sp. strain NRC-1: dimethyl sulfoxide and trimethylamine N-oxide as terminal electron acceptors.
  J Bacteriol, 187, 1659-1667.  
15355966 L.Loschi, S.J.Brokx, T.L.Hills, G.Zhang, M.G.Bertero, A.L.Lovering, J.H.Weiner, and N.C.Strynadka (2004).
Structural and biochemical identification of a novel bacterial oxidoreductase.
  J Biol Chem, 279, 50391-50400.
PDB codes: 1xdq 1xdy
15486691 T.Tomiki, and N.Saitou (2004).
Phylogenetic analysis of proteins associated in the four major energy metabolism systems: photosynthesis, aerobic respiration, denitrification, and sulfur respiration.
  J Mol Evol, 59, 158-176.  
12940994 K.Hatzixanthis, T.Palmer, and F.Sargent (2003).
A subset of bacterial inner membrane proteins integrated by the twin-arginine translocase.
  Mol Microbiol, 49, 1377-1390.  
12910261 M.G.Bertero, R.A.Rothery, M.Palak, C.Hou, D.Lim, F.Blasco, J.H.Weiner, and N.C.Strynadka (2003).
Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A.
  Nat Struct Biol, 10, 681-687.
PDB code: 1q16
12766163 M.Ilbert, V.Méjean, M.T.Giudici-Orticoni, J.P.Samama, and C.Iobbi-Nivol (2003).
Involvement of a mate chaperone (TorD) in the maturation pathway of molybdoenzyme TorA.
  J Biol Chem, 278, 28787-28792.  
12948771 M.Jormakka, B.Byrne, and S.Iwata (2003).
Formate dehydrogenase--a versatile enzyme in changing environments.
  Curr Opin Struct Biol, 13, 418-423.  
12067345 C.A.McDevitt, P.Hugenholtz, G.R.Hanson, and A.G.McEwan (2002).
Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes.
  Mol Microbiol, 44, 1575-1587.  
11844754 S.Gon, J.C.Patte, J.P.Dos Santos, and V.Méjean (2002).
Reconstitution of the trimethylamine oxide reductase regulatory elements of Shewanella oneidensis in Escherichia coli.
  J Bacteriol, 184, 1262-1269.  
12192070 S.Tranier, I.Mortier-Barrière, M.Ilbert, C.Birck, C.Iobbi-Nivol, V.Méjean, and J.P.Samama (2002).
Characterization and multiple molecular forms of TorD from Shewanella massilia, the putative chaperone of the molybdoenzyme TorA.
  Protein Sci, 11, 2148-2157.  
11250197 P.J.Ellis, T.Conrads, R.Hille, and P.Kuhn (2001).
Crystal structure of the 100 kDa arsenite oxidase from Alcaligenes faecalis in two crystal forms at 1.64 A and 2.03 A.
  Structure, 9, 125-132.
PDB codes: 1g8j 1g8k
10652088 B.C.Berks, F.Sargent, and T.Palmer (2000).
The Tat protein export pathway.
  Mol Microbiol, 35, 260-274.  
10747793 C.A.Temple, G.N.George, J.C.Hilton, M.J.George, R.C.Prince, M.J.Barber, and K.V.Rajagopalan (2000).
Structure of the molybdenum site of Rhodobacter sphaeroides biotin sulfoxide reductase.
  Biochemistry, 39, 4046-4052.  
11080634 C.E.Stevenson, F.Sargent, G.Buchanan, T.Palmer, and D.M.Lawson (2000).
Crystal structure of the molybdenum cofactor biosynthesis protein MobA from Escherichia coli at near-atomic resolution.
  Structure, 8, 1115-1125.
PDB code: 1e5k
10735248 C.R.Myers, B.P.Carstens, W.E.Antholine, and J.M.Myers (2000).
Chromium(VI) reductase activity is associated with the cytoplasmic membrane of anaerobically grown Shewanella putrefaciens MR-1.
  J Appl Microbiol, 88, 98.  
10985771 R.C.Bray, B.Adams, A.T.Smith, B.Bennett, and S.Bailey (2000).
Reversible dissociation of thiolate ligands from molybdenum in an enzyme of the dimethyl sulfoxide reductase family.
  Biochemistry, 39, 11258-11269.
PDB codes: 1e5v 1e60 1e61
10702237 S.D.Garton, C.A.Temple, I.K.Dhawan, M.J.Barber, K.V.Rajagopalan, and M.K.Johnson (2000).
Resonance Raman characterization of biotin sulfoxide reductase. Comparing oxomolybdenum enzymes in the ME(2)SO reductase family.
  J Biol Chem, 275, 6798-6805.  
10216869 J.Buc, C.L.Santini, R.Giordani, M.Czjzek, L.F.Wu, and G.Giordano (1999).
Enzymatic and physiological properties of the tungsten-substituted molybdenum TMAO reductase from Escherichia coli.
  Mol Microbiol, 32, 159-168.  
10085074 J.C.Hilton, C.A.Temple, and K.V.Rajagopalan (1999).
Re-design of Rhodobacter sphaeroides dimethyl sulfoxide reductase. Enhancement of adenosine N1-oxide reductase activity.
  J Biol Chem, 274, 8428-8436.  
10411745 M.Ansaldi, C.Bordi, M.Lepelletier, and V.Méjean (1999).
TorC apocytochrome negatively autoregulates the trimethylamine N-oxide (TMAO) reductase operon in Escherichia coli.
  Mol Microbiol, 33, 284-295.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.