8S02 image
Deposition Date 2024-02-13
Release Date 2025-03-05
Last Version Date 2025-09-17
Entry Detail
PDB ID:
8S02
Keywords:
Title:
BzdNO-benzoyl-CoA complex
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.35 Å
R-Value Free:
0.21
R-Value Work:
0.19
R-Value Observed:
0.20
Space Group:
C 1 2 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:BzdO
Gene (Uniprot):bzdO
Chain IDs:A, C
Chain Length:447
Number of Molecules:2
Biological Source:Azoarcus sp. CIB
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:BzdN
Gene (Uniprot):bzdN
Chain IDs:B, D
Chain Length:379
Number of Molecules:2
Biological Source:Azoarcus sp. CIB
Primary Citation
Enzymatic Birch reduction via hydrogen atom transfer at [4Fe-4S]-OH 2 and [8Fe-9S] clusters.
Nat Commun 16 3236 3236 (2025)
PMID: 40185728 DOI: 10.1038/s41467-025-58418-w

Abstact

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.

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