8S02 | pdb_00008s02

BzdNO-benzoyl-CoA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.217 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Enzymatic Birch reduction via hydrogen atom transfer at [4Fe-4S]-OH 2 and [8Fe-9S] clusters.

Fuchs, J.Fernandez-Arevalo, U.Demmer, U.Diaz, E.Ullmann, G.M.Pierik, A.J.Ermler, U.Boll, M.

(2025) Nat Commun 16: 3236-3236

  • DOI: https://doi.org/10.1038/s41467-025-58418-w
  • Primary Citation of Related Structures:  
    8S02, 8S1T, 8S2R

  • PubMed Abstract: 

    The alkali metal- and ammonia-dependent Birch reduction is the classical synthetic method for achieving dihydro additions to arenes, typically yielding 1,4-cyclodienes. A mild biological alternative to this process are 1,5-dienoyl-coenzyme A (CoA)-forming class I and II benzoyl-CoA reductases (BCRs), widely abundant key enzymes in the biodegradation of aromatic compounds at anoxic environments. To obtain a comprehensive mechanistic understanding of class I BCR catalysis, we produced the active site subunits from a denitrifying bacterium and determined the X-ray structure of its substrate and product complexes at 1.4 Å revealing non-canonical double-cubane [8Fe-9S] and active site aqua-[4Fe-4S] clusters. Together with kinetic, spectroscopic and QM/MM studies, we provide evidence for a radical mechanism with a [4Fe-4S] cluster-bound water molecule acting as hydrogen atom and electron donor at potentials beyond the biological redox window. An analogous Birch-like radical mechanism is applied by class II BCRs with the catalytic water bound to a tungsten-bis-metallopterin cofactor. The use of activated, metal-bound water ligands as hydrogen atom donor serves as a basic blueprint for future enzymatic or biomimetic Birch reduction processes.


  • Organizational Affiliation
    • Faculty of Biology - Microbiology, University of Freiburg, 79104, Freiburg, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BzdO
A, C
447Azoarcus sp. CIBMutation(s): 0 
Gene Names: bzdO
UniProt
Find proteins for Q68VL9 (Aromatoleum sp. (strain CIB))
Explore Q68VL9 
Go to UniProtKB:  Q68VL9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ68VL9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BzdN
B, D
379Azoarcus sp. CIBMutation(s): 0 
Gene Names: bzdN
UniProt
Find proteins for Q68VM0 (Aromatoleum sp. (strain CIB))
Explore Q68VM0 
Go to UniProtKB:  Q68VM0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ68VM0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BYC
Query on BYC

Download Ideal Coordinates CCD File 
E [auth A],
J [auth C]
benzoyl coenzyme A
C28 H40 N7 O17 P3 S
VEVJTUNLALKRNO-TYHXJLICSA-N
BJ8
Query on BJ8

Download Ideal Coordinates CCD File 
H [auth B],
O [auth D]
Double cubane cluster
Fe8 S9
CSVVAMDLRWBOEA-UHFFFAOYSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
G [auth A],
N [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
I [auth B],
K [auth C]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
L [auth C],
M [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.217 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.85α = 90
b = 102.79β = 102.48
c = 86.82γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-09-17
    Changes: Database references