8S2R | pdb_00008s2r

BzdNO in partially coenzyme A - free state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.211 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8S2R

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 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.

Macromolecule Content 

  • Total Structure Weight: 193.95 kDa 
  • Atom Count: 14,200 
  • Modeled Residue Count: 1,617 
  • Deposited Residue Count: 1,652 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BzdO
A, C
447Azoarcus sp. CIBMutation(s): 0 
Gene Names: bzdO
UniProt
Find proteins for A0ACD6B855 (Aromatoleum sp. (strain CIB))
Explore A0ACD6B855 
Go to UniProtKB:  A0ACD6B855
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B855
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
BzdN
B, D
379Azoarcus sp. CIBMutation(s): 0 
Gene Names: bzdN
UniProt
Find proteins for A0ACD6B854 (Aromatoleum sp. (strain CIB))
Explore A0ACD6B854 
Go to UniProtKB:  A0ACD6B854
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B854
Sequence Annotations
Expand
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],
N [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],
M [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
I [auth B],
O [auth D]
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],
K [auth C],
L [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.17α = 90
b = 102.71β = 102.48
c = 86.9γ = 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