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: 2.21 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: https://doi.org/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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Benzoyl-CoA reductase, putative
A, B, C, D
653Geobacter metallireducens GS-15Mutation(s): 0 
Gene Names: bamB-1, Gmet_2087
UniProt
Find proteins for Q39TV8 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15))
Explore Q39TV8 
Go to UniProtKB:  Q39TV8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39TV8
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein
E, F, G, H
179Geobacter metallireducens GS-15Mutation(s): 0 
Gene Names: bamC-1, Gmet_2086
UniProt
Find proteins for Q39TV9 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15))
Explore Q39TV9 
Go to UniProtKB:  Q39TV9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39TV9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4KX
Query on 4KX
Download Ideal Coordinates CCD File 
CA [auth C],
JA [auth D],
O [auth A],
V [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 
FA [auth D]
GA [auth D]
J [auth A]
K [auth A]
Q [auth B]
FA [auth D],
GA [auth D],
J [auth A],
K [auth A],
Q [auth B],
R [auth B],
X [auth C],
Y [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 
EA [auth D]
I [auth A]
KA [auth E]
LA [auth E]
MA [auth E]
EA [auth D],
I [auth A],
KA [auth E],
LA [auth E],
MA [auth E],
NA [auth F],
OA [auth F],
P [auth B],
PA [auth F],
QA [auth G],
RA [auth G],
SA [auth G],
TA [auth H],
UA [auth H],
VA [auth H],
W [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
W
Query on W
Download Ideal Coordinates CCD File 
BA [auth C],
HA [auth D],
L [auth A],
S [auth B]		TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
IA [auth D],
M [auth A],
T [auth B],
Z [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
UNL
Query on UNL
Download Ideal Coordinates CCD File 
AA [auth C],
DA [auth D],
N [auth A],
U [auth B]		Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.34α = 90
b = 116.3β = 110.48
c = 144.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

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

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