3I39

NI,FE-CODH-320 MV+CN state

Summary for 3I39

• Entry DOI: 10.2210/pdb3i39/pdb
• Related: 3B51 3B52 3B53
• Descriptor: Carbon monoxide dehydrogenase 2, IRON/SULFUR CLUSTER, FE2/S2 (INORGANIC) CLUSTER, ... (7 entities in total)
• Functional Keywords: cyanide, cluster c, iron, iron-sulfur, membrane, metal-binding, nickel, oxidoreductase, cell inner membrane, cell membrane
• Biological source: Carboxydothermus hydrogenoformans
• Total number of polymer chains: 1
• Total formula weight: 70211.55

Authors

Jeoung, J.-H.,Dobbek, H. (deposition date: 2009-06-30, release date: 2009-08-11, Last modification date: 2024-02-21)

Primary citation

Jeoung, J.H.,Dobbek, H.
Structural basis of cyanide inhibition of Ni, Fe-containing carbon monoxide dehydrogenase
J.Am.Chem.Soc., 131:9922-9923, 2009

PubMed Abstract: Carbon monoxide dehydrogenases (CODHs) catalyze the reversible oxidation of carbon monoxide with water to carbon dioxide, two protons, and two electrons. The CODHs of anaerobic microorganisms harbor a complex Ni/Fe/S-containing metal center called a C-cluster in their active site, which activates the substrates water and carbon monoxide, stabilizes an intermediary metal-carboxylate, and transiently stores the two electrons generated in the reaction. Several small molecules have been reported to inhibit carbon monoxide oxidation by CODHs, among which the cyanide anion acts as a slow binding inhibitor. Cyanide is isoelectronic to the substrate carbon monoxide, and its binding to the C-cluster has been reported to involve nickel, nickel and iron, or only iron. We report the crystal structure of CODH-II from Carboxydothermus hydrogenoformans in complex with cyanide at 1.36 A resolution. The structure reveals that cyanide binds to the C-cluster at an open coordination site completing the square-planar coordination geometry of the nickel ion. While active CODH has a water/hydroxo-ligand bound to an iron ion near nickel, in the cyanide complex the water/hydroxo-ligand is lost and iron occupies a position more close to the nickel ion. Based on the structure, we suggest that the competitive inhibitory character of cyanide originates from it obstruction of carbon monoxide binding to the nickel ion while the slow binding inhibition is due to a conformational change of the protein during which the water/hydroxo-ligand bound to iron is lost.

PubMed: 19583208
DOI: 10.1021/ja9046476

Experimental method

X-RAY DIFFRACTION (1.36 Å)