28LW

CryoEM structure of carbon monoxide dehydrogenase from Ruminococcus flavefaciens

Summary for 28LW

• Entry DOI: 10.2210/pdb28lw/pdb
• EMDB information: 56604
• Descriptor: anaerobic carbon-monoxide dehydrogenase, IRON/SULFUR CLUSTER (2 entities in total)
• Functional Keywords: carbon monoxide dehydrogenase, codh, metalloenzyme, iron sulfur protein, anaerobic enzyme, oxidoreductase
• Biological source: Ruminococcus flavefaciens ATCC 19208
• Total number of polymer chains: 2
• Total formula weight: 159009.42

Authors

Srinivas, V.,Hogbom, M. (deposition date: 2026-02-06, release date: 2026-09-23)

Primary citation

Bohm, M.,Srinivas, V.,Wiseman, B.,Huang, P.,Senger, M.,Hogbom, M.,Land, H.
Beyond Canonical CO Oxidation: Structural and Evolutionary Insights Into a Non-Canonical Carbon Monoxide Dehydrogenase.
Angew.Chem.Int.Ed.Engl., :e1702233-e1702233, 2026

PubMed Abstract: Carbon monoxide dehydrogenases (CODHs) catalyse the reversible oxidation of CO to CO and play central roles in microbial carbon metabolism. While well-characterised CODHs from different phylogenetic backgrounds exhibit high bidirectional activity, the enigmatic clade B remains functionally uncharacterised. Here, we present the first structural and biochemical characterisation of a clade B CODH from Ruminococcus flavefaciens (RfCODH). It reveals striking divergence from canonical enzymes. A new anaerobic cryo-EM workflow was developed, carried out entirely under anoxic conditions by manual blotting and plunge freezing. It resulted in a 2.53 Å RfCODH structure. The structure adopts the typical CODH fold, but exhibits blocked gas channels, a compromised proton transfer pathway and disrupted cofactor coordination. This provides a structural rationale for RfCODH's severely attenuated CO oxidation activity (13 mU/mg vs. 900 U/mg for the well-studied ChCODH-II). EPR spectroscopy reveals unique oxidised C-cluster states not previously characterised in CODHs. Mirror tree analysis hints to co-evolution between clade B CODHs and associated ABC transporter substrate-binding proteins, suggesting these enzymes function in metabolism of substrates imported via the ABC transporter module. All findings indicate evolutionary repurposing of the CODH scaffold for alternative physiological functions.

PubMed: 42495917
DOI: 10.1002/anie.1702233

Experimental method

ELECTRON MICROSCOPY (2.55 Å)