4Z3W | pdb_00004z3w

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 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4Z3W

This is version 1.4 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 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. 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.

Macromolecule Content 

  • Total Structure Weight: 389.23 kDa 
  • Atom Count: 26,926 
  • Modeled Residue Count: 3,272 
  • Deposited Residue Count: 3,328 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Benzoyl-CoA reductase, putative
A, B, C, D
653Geobacter metallireducens GS-15Mutation(s): 0 
Gene Names: bamB-1Gmet_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
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence 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-1Gmet_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
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / 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
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
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-UHFFFAOYSA-N
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
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
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free:  0.222 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
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

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyBO 1565/10-2
German Research FoundationGermanyER 222/5-2
Swiss National Science FoundationSwitzerlandP1SKP3-198452
Swiss National Science FoundationSwitzerlandP1SKP3-155073

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
  • Version 1.4: 2024-01-10
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description