1O94

Ternary complex between trimethylamine dehydrogenase and electron transferring flavoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Extensive Conformational Sampling in a Ternary Electron Transfer Complex.

Leys, D.Basran, J.Talfournier, F.Sutcliffe, M.J.Scrutton, N.S.

(2003) Nat.Struct.Mol.Biol. 10: 219

  • DOI: 10.1038/nsb894
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Here we report the crystal structures of a ternary electron transfer complex showing extensive motion at the protein interface. This physiological complex comprises the iron-sulfur flavoprotein trimethylamine dehydrogenase and electron transferring f ...

    Here we report the crystal structures of a ternary electron transfer complex showing extensive motion at the protein interface. This physiological complex comprises the iron-sulfur flavoprotein trimethylamine dehydrogenase and electron transferring flavoprotein (ETF) from Methylophilus methylotrophus. In addition, we report the crystal structure of free ETF. In the complex, electron density for the FAD domain of ETF is absent, indicating high mobility. Positions for the FAD domain are revealed by molecular dynamics simulation, consistent with crystal structures and kinetic data. A dual interaction of ETF with trimethylamine dehydrogenase provides for dynamical motion at the protein interface: one site acts as an anchor, thereby allowing the other site to sample a large range of interactions, some compatible with rapid electron transfer. This study establishes the role of conformational sampling in multi-domain redox systems, providing insight into electron transfer between ETFs and structurally distinct redox partners.


    Organizational Affiliation

    Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, UK. dl37@le.ac.uk




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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ELECTRON TRANSFER FLAVOPROTEIN BETA-SUBUNIT
C, E
264Methylophilus methylotrophusMutation(s): 0 
Gene Names: etfB
Find proteins for P53570 (Methylophilus methylotrophus)
Go to UniProtKB:  P53570
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ELECTRON TRANSFER FLAVOPROTEIN ALPHA-SUBUNIT
D, F
320Methylophilus methylotrophusMutation(s): 0 
Gene Names: etfA
Find proteins for P53571 (Methylophilus methylotrophus)
Go to UniProtKB:  P53571
Small Molecules
Ligands 4 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

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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
AMP
Query on AMP

Download SDF File 
Download CCD File 
C, E
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 118.930α = 90.00
b = 211.543β = 100.03
c = 125.970γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-06
    Type: Initial release
  • Version 1.1: 2013-09-18
    Type: Derived calculations, Non-polymer description, Other, Version format compliance