4Z3W

Active site complex BamBC of Benzoyl Coenzyme A reductase in complex with 1,5 Dienoyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.208 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.178 

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

    Max Planck Institute of Biophysics, Frankfurt, Germany.




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 5 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

Download SDF File 
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

Download SDF File 
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
MG
Query on MG

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

Download SDF File 
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: 2.208 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 125.340α = 90.00
b = 116.300β = 110.48
c = 144.160γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DFGGermanyBO 1565/10-2
DFGGermanyER 222/5-2
SNFSwitzerlandP1SKP3-198452
SNFSwitzerlandP1SKP3-155073

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