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 
  • R-Value Observed: 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:  
    4Z3W, 4Z3X, 4Z3Y, 4Z3Z, 4Z40

  • 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) that have a key role in the globally important bacterial degradation of aromatic compounds at anoxic sites ...

    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

    Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Benzoyl-CoA reductase, putativeA, B, C, D653Geobacter metallireducens GS-15Mutation(s): 0 
Gene Names: bamB-1Gmet_2087
Find proteins for Q39TV8 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15))
Explore Q39TV8 
Go to UniProtKB:  Q39TV8
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer proteinE, F, G, H179Geobacter metallireducens GS-15Mutation(s): 0 
Gene Names: bamC-1Gmet_2086
Find proteins for Q39TV9 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15))
Explore Q39TV9 
Go to UniProtKB:  Q39TV9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4KX
Query on 4KX

Download Ideal Coordinates CCD File 
EA [auth C], NA [auth D], Q [auth A], X [auth B]1,5 Dienoyl-CoA
C28 H42 N7 O17 P3 S
IHXBZDHPKCDGKN-TYHXJLICSA-N
 Ligand Interaction
MTE
Query on MTE

Download Ideal Coordinates CCD File 
AA [auth C], HA [auth D], IA [auth D], J [auth A], K [auth A], S [auth B], T [auth B], Z [auth C]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
SF4
Query on SF4

Download Ideal Coordinates CCD File 
GA [auth D] , I [auth A] , OA [auth E] , PA [auth E] , QA [auth E] , R [auth B] , RA [auth F] , SA [auth F] , 
GA [auth D],  I [auth A],  OA [auth E],  PA [auth E],  QA [auth E],  R [auth B],  RA [auth F],  SA [auth F],  TA [auth F],  UA [auth G],  VA [auth G],  WA [auth G],  XA [auth H],  Y [auth C],  YA [auth H],  ZA [auth H]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
MA [auth D]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
W
Query on W

Download Ideal Coordinates CCD File 
DA [auth C], JA [auth D], L [auth A], U [auth B]TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
LA [auth D], O [auth A], P [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth C], KA [auth D], M [auth A], W [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

Download Ideal Coordinates CCD File 
CA [auth C], FA [auth D], N [auth A], V [auth B]Unknown ligand
JLVVSXFLKOJNIY-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 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.767α = 90
b = 116.256β = 110.43
c = 143.973γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHASERphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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