4Z3X

Active site complex BamBC of Benzoyl Coenzyme A reductase in complex with 1-Monoenoyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of enzymatic benzene ring reduction.

Weinert, T.Huwiler, S.G.Kung, J.W.Weidenweber, S.Hellwig, P.Stark, H.J.Biskup, T.Weber, S.Cotelesage, J.J.George, G.N.Ermler, U.Boll, M.

(2015) Nat.Chem.Biol. 11: 586-591

  • DOI: 10.1038/nchembio.1849
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In chemical synthesis, the widely used Birch reduction of aromatic compounds to cyclic dienes requires alkali metals in ammonia as extremely low-potential electron donors. An analogous reaction is catalyzed by benzoyl-coenzyme A reductases (BCRs) tha ...

    In chemical synthesis, the widely used Birch reduction of aromatic compounds to cyclic dienes requires alkali metals in ammonia as extremely low-potential electron donors. An analogous reaction is catalyzed by benzoyl-coenzyme A reductases (BCRs) that have a key role in the globally important bacterial degradation of aromatic compounds at anoxic sites. Because of the lack of structural information, the catalytic mechanism of enzymatic benzene ring reduction remained obscure. Here, we present the structural characterization of a dearomatizing BCR containing an unprecedented tungsten cofactor that transfers electrons to the benzene ring in an aprotic cavity. Substrate binding induces proton transfer from the bulk solvent to the active site by expelling a Zn(2+) that is crucial for active site encapsulation. Our results shed light on the structural basis of an electron transfer process at the negative redox potential limit in biology. They open the door for biological or biomimetic alternatives to a basic chemical synthetic tool.


    Organizational Affiliation

    Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, Strasbourg, France.,Max Planck Institute of Biophysics, Frankfurt, Germany.,Department of Analytical Chemistry, Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany.,Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany.,Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany.,1] Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada. [2] Canadian Light Source, Saskatoon, Saskatchewan, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Benzoyl-CoA reductase, putative
A, B, C, D
653Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210)Mutation(s): 0 
Gene Names: bamB-1
Find proteins for Q39TV8 (Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210))
Go to UniProtKB:  Q39TV8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein
E, F, G, H
179Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210)Mutation(s): 0 
Gene Names: bamC-1
Find proteins for Q39TV9 (Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210))
Go to UniProtKB:  Q39TV9
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
4KX
Query on 4KX

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Download CCD File 
A, B, C, D
1,5 Dienoyl-CoA
Cyclohex-1,5-diene-1-carbonyl-CoA
C28 H42 N7 O17 P3 S
IHXBZDHPKCDGKN-TYHXJLICSA-N
 Ligand Interaction
MTE
Query on MTE

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Download CCD File 
A, B, C, D
PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C10 H14 N5 O6 P S2
HPEUEJRPDGMIMY-IFQPEPLCSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
D
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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Download CCD File 
A, D
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
W
Query on W

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Download CCD File 
A, B, C, D
TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 125.767α = 90.00
b = 116.256β = 110.43
c = 143.973γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XSCALEdata scaling
Cootmodel building
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2015-07-01
    Type: Database references
  • Version 1.2: 2015-07-08
    Type: Database references
  • Version 1.3: 2015-07-29
    Type: Database references