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PDBsum entry 2tmd

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
2tmd
Jmol
Contents
Protein chains
729 a.a. *
Ligands
SF4 ×2
FMN ×2
ADP ×2
Waters ×581
* Residue conservation analysis
PDB id:
2tmd
Name: Oxidoreductase
Title: Correlation of x-ray deduced and experimental amino acid seq trimethylamine dehydrogenase
Structure: Trimethylamine dehydrogenase. Chain: a, b. Engineered: yes
Source: Methylophilus methylotrophus. Organism_taxid: 2327. Strain: w3a1
Biol. unit: Dimer (from PQS)
Resolution:
2.40Å     R-factor:   0.154    
Authors: F.S.Mathews,L.W.Lim,S.White
Key ref: M.J.Barber et al. (1992). Correlation of x-ray deduced and experimental amino acid sequences of trimethylamine dehydrogenase. J Biol Chem, 267, 6611-6619. PubMed id: 1551870
Date:
15-Oct-93     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P16099  (DHTM_METME) -  Trimethylamine dehydrogenase
Seq:
Struc:
 
Seq:
Struc:
730 a.a.
729 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.5.8.2  - Trimethylamine dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Trimethylamine + H2O + electron-transferring flavoprotein = dimethylamine + formaldehyde + reduced electron-transferring flavoprotein
Trimethylamine
+ H(2)O
+ electron-transferring flavoprotein
= dimethylamine
+ formaldehyde
+ reduced electron-transferring flavoprotein
      Cofactor: FMN; Iron-sulfur
FMN
Bound ligand (Het Group name = FMN) corresponds exactly
Iron-sulfur
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
J Biol Chem 267:6611-6619 (1992)
PubMed id: 1551870  
 
 
Correlation of x-ray deduced and experimental amino acid sequences of trimethylamine dehydrogenase.
M.J.Barber, P.J.Neame, L.W.Lim, S.White, F.S.Matthews.
 
  ABSTRACT  
 
The amino acid sequence of the iron-sulfur-flavoprotein, trimethylamine dehydrogenase, isolated from the bacterium W3A1 has been deduced from the x-ray diffraction pattern obtained at 2.4-A resolution. This sequence has been compared to portions of the primary sequence derived by gas-phase sequencing of isolated peptides obtained from cyanogen bromide and endoprotease Arg-C and Asp-N digestions of the purified enzyme. A consensus sequence has resulted and is comprised of 729 amino acids with Ala at both NH2- and COOH-terminal positions. The consensus sequence contains 13 cysteine residues. Approximately 80% of the sequence has been confirmed by direct sequencing with approximately 81% agreement with the x-ray deduced sequence. The calculated subunit molecular mass of the apoenzyme is 78,899 Da, in good agreement with published values of approximately 83,000. The anomalous scattering map from the native protein has also been shown to provide accurate information about the positions of most of the weak anomalous scattering centers such as sulfur or phosphorus atoms and to complement x-ray or chemical sequencing methods.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19846434 M.Tsutsumi, N.Tsuse, N.Fujieda, and K.Kano (2010).
Site-directed mutation at residues near the catalytic site of histamine dehydrogenase from Nocardioides simplex and its effects on substrate inhibition.
  J Biochem, 147, 257-264.  
19651103 P.F.Fitzpatrick (2010).
Oxidation of amines by flavoproteins.
  Arch Biochem Biophys, 493, 13-25.  
19217394 A.R.Kinjo, and H.Nakamura (2009).
Comprehensive structural classification of ligand-binding motifs in proteins.
  Structure, 17, 234-246.  
11761328 D.E.Edmondson, and P.Newton-Vinson (2001).
The covalent FAD of monoamine oxidase: structural and functional role and mechanism of the flavinylation reaction.
  Antioxid Redox Signal, 3, 789-806.  
10651042 O.Vallon (2000).
New sequence motifs in flavoproteins: evidence for common ancestry and tools to predict structure.
  Proteins, 38, 95.  
10869173 P.Trickey, J.Basran, L.Y.Lian, Z.Chen, J.D.Barton, M.J.Sutcliffe, N.S.Scrutton, and F.S.Mathews (2000).
Structural and biochemical characterization of recombinant wild type and a C30A mutant of trimethylamine dehydrogenase from methylophilus methylotrophus (sp. W(3)A(1)).
  Biochemistry, 39, 7678-7688.
PDB codes: 1djn 1djq
9283290 C.Liang, and K.Mislow (1997).
Topological chirality of iron-sulfur proteins.
  Biopolymers, 42, 411-414.  
  9300484 S.Raychaudhuri, F.Younas, P.A.Karplus, C.H.Faerman, and D.R.Ripoll (1997).
Backbone makes a significant contribution to the electrostatics of alpha/beta-barrel proteins.
  Protein Sci, 6, 1849-1857.  
  8880899 G.Van Driessche, M.Koh, Z.W.Chen, F.S.Mathews, T.E.Meyer, R.G.Bartsch, M.A.Cusanovich, and J.J.Van Beeumen (1996).
Covalent structure of the flavoprotein subunit of the flavocytochrome c: sulfide dehydrogenase from the purple phototrophic bacterium Chromatium vinosum.
  Protein Sci, 5, 1753-1764.  
  8762144 S.Janecek (1996).
Invariant glycines and prolines flanking in loops the strand beta 2 of various (alpha/beta)8-barrel enzymes: a hidden homology?
  Protein Sci, 5, 1136-1143.  
8710828 T.Madej, J.F.Gibrat, and S.H.Bryant (1995).
Threading a database of protein cores.
  Proteins, 23, 356-369.  
8592705 T.Sandalova, and Y.Lindqvist (1995).
Three-dimensional model of the alpha-subunit of bacterial luciferase.
  Proteins, 23, 241-255.  
8306995 S.I.Goodman, K.M.Axtell, L.A.Bindoff, S.E.Beard, R.E.Gill, and F.E.Frerman (1994).
Molecular cloning and expression of a cDNA encoding human electron transfer flavoprotein-ubiquinone oxidoreductase.
  Eur J Biochem, 219, 277-286.  
  8491719 C.V.Franklund, S.F.Baron, and P.B.Hylemon (1993).
Characterization of the baiH gene encoding a bile acid-inducible NADH:flavin oxidoreductase from Eubacterium sp. strain VPI 12708.
  J Bacteriol, 175, 3002-3012.  
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 codes are shown on the right.