2YIV

NI,FE-CODH with n-butylisocyanate state

Summary for 2YIV

• Entry DOI: 10.2210/pdb2yiv/pdb
• Related: 1SU6 1SU7 1SU8 1SUF
• Descriptor: CARBON MONOXIDE DEHYDROGENASE 2, IRON/SULFUR CLUSTER, FE2/S2 (INORGANIC) CLUSTER, ... (8 entities in total)
• Functional Keywords: oxidoreductase
• Biological source: CARBOXYDOTHERMUS HYDROGENOFORMANS
• Cellular location: Cytoplasm: Q9F8A8
• Total number of polymer chains: 1
• Total formula weight: 70313.96

Authors

Jeoung, J.H.,Dobbek, H. (deposition date: 2011-05-16, release date: 2012-03-28, Last modification date: 2023-12-20)

Primary citation

Jeoung, J.H.,Dobbek, H.
N-Butyl Isocyanide Oxidation at the [Nife4S4Oh(X)] Cluster of Co Dehydrogenase.
J.Biol.Inorg.Chem., 17:167-, 2012

PubMed Abstract: Carbon monoxide dehydrogenases (CODHs) catalyze the reversible oxidation of carbon monoxide by reaction with water to yield carbon dioxide, two protons, and two electrons. Two principal types of CODHs can be distinguished. Ni,Fe-containing CODHs contain a [NiFe(4)S(4)OH(x)] cluster within their active site, to which the direct binding of the substrates water and carbon dioxide has been revealed by protein X-ray crystallography. n-Butyl isocyanide is a slow-turnover substrate of CODHs, whose oxidation at the active site shows several parallels to the oxidation of carbon monoxide. Here, we report the crystal structure of CODH-II from Carboxydothermus hydrogenoformans resulting from the enzymatic oxidation of n-butyl isocyanide to n-butyl isocyanate at its active site cluster. The high resolution of the structure (d(min) = 1.28 Å) revealed n-butyl isocyanate bound to the active site cluster and identified a novel type of Ni-C bond in CODHs. The structure suggests the occurrence of tetrahedral in addition to square-planar nickel complexes in product-bound states of this enzyme. Furthermore, we discovered a molecule of n-butyl isocyanide in a hydrophobic channel leading to the active site, revealing a unique architecture for the substrate channel of CODH-II compared with the bifunctional CODHs.

PubMed: 21904889
DOI: 10.1007/S00775-011-0839-Y

Experimental method

X-RAY DIFFRACTION (1.28 Å)