2TMD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.154 
  • R-Value Observed: 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

  • Primary Citation of Related Structures:  
    2TMD

  • 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 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 ...

    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
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRIMETHYLAMINE DEHYDROGENASEA, B729Methylophilus methylotrophus W3A1Mutation(s): 0 
EC: 1.5.99.7 (PDB Primary Data), 1.5.8.2 (UniProt)
UniProt
Find proteins for P16099 (Methylophilus methylotrophus)
Explore P16099 
Go to UniProtKB:  P16099
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16099
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
ADP
Query on ADP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.75α = 90
b = 71.95β = 97.69
c = 83.82γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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