9RJT

W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - Dithionite reduced - anaerobic soaked with 58 bar CO2 for 1 min

Summary for 9RJT

• Entry DOI: 10.2210/pdb9rjt/pdb
• Descriptor: Formate dehydrogenase, alpha subunit, selenocysteine-containing, Formate dehydrogenase, beta subunit, putative, 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE, ... (10 entities in total)
• Functional Keywords: formate, co2, molybdenum and tungsten enzymes, dmso reductase family, electron transport, oxidoreductase
• Biological source: Nitratidesulfovibrio vulgaris str. Hildenborough; More
• Total number of polymer chains: 2
• Total formula weight: 141006.84

Authors

Vilela-Alves, G.,Manuel, R.R.,Carpentier, P.,Pereira, I.C.,Romao, M.J.,Mota, C. (deposition date: 2025-06-12, release date: 2026-03-04, Last modification date: 2026-04-29)

Primary citation

Vilela-Alves, G.,Manuel, R.R.,Martins, G.,Carpentier, P.,Raczynska, A.,Szaleniec, M.,Pereira, I.A.C.,Romao, M.J.,Mota, C.
Structural Insights Into CO 2 Transport Pathways in a W-Formate Dehydrogenase: Structural Basis for CO 2 Reduction.
Angew.Chem.Int.Ed.Engl., 65:e26133-e26133, 2026

PubMed Abstract: Mo/W-dependent formate dehydrogenases (Fdhs) catalyze the reversible reduction of CO to formate and are key biocatalysts with high potential for CO capture/conversion technologies. Although previous studies have suggested the presence of two substrate-access tunnels in Fdhs, experimental evidence for CO-specific pathways has been lacking. Here, we present an integrated study of Nitratidesulfovibrio vulgaris FdhAB combining crystallography, molecular dynamics simulations, mutagenesis, and kinetic assays. NvFdhAB crystals pressurized with Kr, O, and CO were used to map gas diffusion routes and uncovered a substrate-retention site consistently occupied by small molecules in multiple crystal structures. Our results indicate that both substrates mostly use the main tunnel to reach this retention site, but HO and CO can also enter through a novel side branch before following a shared route to the buried W active site. The retention site, located at the junction of both tunnels, plays a synergistic role in enhancing CO reduction by increasing substrate concentration near the catalytic center, thereby improving catalytic efficiency. Notably, variants affecting this site showed a selective effect for CO reduction, with no impact on formate oxidation. These findings provide experimental evidence of a CO-specific pathway and identify structural determinants underpinning efficient CO reduction in this enzyme family.

PubMed: 41787858
DOI: 10.1002/anie.202526133

Experimental method

X-RAY DIFFRACTION (1.83 Å)