9G7J | pdb_00009g7j

Crystal structure of the tungsten-dependent aldehyde:ferredoxin oxidoreductase from Clostridium autoethanogenum.

PDB DOI: https://doi.org/10.2210/pdb9G7J/pdb

Classification: OXIDOREDUCTASE
Organism(s): Clostridium autoethanogenum DSM 10061
Mutation(s): No

Deposited: 2024-07-21 Released: 2025-05-28
Deposition Author(s): Lemaire, O.N., Wagner, T.
Funding Organization(s): Max Planck Society, German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.178 (Depositor), 0.178 (DCC)
R-Value Work:
0.162 (Depositor), 0.162 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Carbon-monoxide-driven bioethanol production operates through a tungsten-dependent catalyst.

Lemaire, O.N., Belhamri, M., Shevchenko, A., Wagner, T.

(2025) Nat Chem Biol

PubMed: 41162695 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41589-025-02055-3
Primary Citation of Related Structures:
9G7J

PubMed Abstract:
Microbial alcohol production from waste gases is a game changer for sustainable carbon cycling and remediation. While the biotechnological process using Clostridium autoethanogenum to transform syngas (H ₂, CO ₂ and CO) is blooming, scientific debates remain on the ethanol biosynthesis pathway. Here, we experimentally validated that ethanol production is initiated through a tungsten-dependent aldehyde:ferredoxin oxidoreductase (AFOR), which reduces acetate to acetaldehyde. The reaction, thermodynamically unfavorable under standard conditions, has been considered by many as unsuitable in vivo but is rather approved by metabolic modeling. To answer this riddle, we demonstrated that the thermodynamic coupling of CO oxidation and ethanol synthesis allows acetate reduction. The experiments, performed with native CO dehydrogenase and AFOR, highlighted the key role of ferredoxin in stimulating the activity of both metalloenzymes and electron shuttling. The crystal structure of holo AFOR, refined to 1.59-Å resolution, and its biochemical characterization provide new insights into the cofactor chemistry and the specificities of this enzyme, fundamental to sustainable biofuel production.

Organizational Affiliation

Max Planck Institute for Marine Microbiology, Bremen, Germany. olemaire@mpi-bremen.de.

Macromolecule Content

Total Structure Weight: 135.77 kDa
Atom Count: 11,010
Modeled Residue Count: 1,214
Deposited Residue Count: 1,214
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde ferredoxin oxidoreductase	A, B	607	Clostridium autoethanogenum DSM 10061	Mutation(s): 0 EC: 1
UniProt
Find proteins for A0A3M0S906 (Clostridium autoethanogenum) Explore A0A3M0S906 Go to UniProtKB: A0A3M0S906
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3M0S906
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IJH (Subject of Investigation/LOI) Query on A1IJH Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	Tungstopterin cofactor C₂₀ H₂₂ Mg N₁₀ O₁₂ P₂ S₄ W TXTOFHXWJBZWPO-BURDSJQCSA-H		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	I [auth B], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]