2TMD

CORRELATION OF X-RAY DEDUCED AND EXPERIMENTAL AMINO ACID SEQUENCES OF TRIMETHYLAMINE DEHYDROGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Correlation of x-ray deduced and experimental amino acid sequences of trimethylamine dehydrogenase.

Barber, M.J.Neame, P.J.Lim, L.W.White, S.Matthews, F.S.

(1992) J.Biol.Chem. 267: 6611-6619


  • PubMed 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 t ...

    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.


    Related Citations: 
    • Studies of Crystalline Trimethylamine Dehydrogenase in Three Oxidation States and in the Presence of Substrate and Inhibitor
      Bellamy, H.D.,Lim, L.W.,Mathews, F.S.,Dunham, W.R.
      (1989) J.Biol.Chem. 264: 11887
    • Three-Dimensional Structure of the Iron-Sulfur Flavoprotein Trimethylamine Dehydrogenase at 2.4 Angstroms Resolution
      Lim, L.W.,Shamala, N.,Mathews, F.S.,Steenkamp, D.J.,Hamlin, R.,Xuong, N.H.
      (1986) J.Biol.Chem. 261: 15140
    • Identification of Adp in the Iron-Sulfur Flavoprotein Trimethylamine Dehydrogenase
      Lim, L.W.,Mathews, F.S.,Steenkamp, D.J.
      (1988) J.Biol.Chem. 263: 3075


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of South Florida, College of Medicine, Tampa 33612.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRIMETHYLAMINE DEHYDROGENASE
A, B
729Methylophilus methylotrophusMutation(s): 0 
Gene Names: tmd
EC: 1.5.8.2
Find proteins for P16099 (Methylophilus methylotrophus)
Go to UniProtKB:  P16099
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 147.750α = 90.00
b = 71.950β = 97.69
c = 83.820γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance