3I04

Cyanide-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica, cyanide-bound C-cluster

Summary for 3I04

• Entry DOI: 10.2210/pdb3i04/pdb
• Related: 1MJG 3I01
• Descriptor: Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta, SODIUM ION, Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha, ... (11 entities in total)
• Functional Keywords: protein-protein complex, carbon dioxide fixation, electron transport, iron, iron-sulfur, metal-binding, nickel, oxidoreductase, transport, transferase, oxidoreductase-transferase complex, oxidoreductase/transferase
• Biological source: Moorella thermoacetica (Clostridium thermoaceticum); More
• Total number of polymer chains: 8
• Total formula weight: 624693.14

Authors

Kung, Y.,Doukov, T.I.,Drennan, C.L. (deposition date: 2009-06-24, release date: 2009-09-01, Last modification date: 2023-09-06)

Primary citation

Kung, Y.,Doukov, T.I.,Seravalli, J.,Ragsdale, S.W.,Drennan, C.L.
Crystallographic snapshots of cyanide- and water-bound C-clusters from bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase.
Biochemistry, 48:7432-7440, 2009

PubMed Abstract: Nickel-containing carbon monoxide dehydrogenases (CODHs) reversibly catalyze the oxidation of carbon monoxide to carbon dioxide and are of vital importance in the global carbon cycle. The unusual catalytic CODH C-cluster has been crystallographically characterized as either a NiFe(4)S(4) or a NiFe(4)S(5) metal center, the latter containing a fifth, additional sulfide that bridges Ni and a unique Fe site. To determine whether this bridging sulfide is catalytically relevant and to further explore the mechanism of the C-cluster, we obtained crystal structures of the 310 kDa bifunctional CODH/acetyl-CoA synthase complex from Moorella thermoacetica bound both with a substrate H(2)O/OH(-) molecule and with a cyanide inhibitor. X-ray diffraction data were collected from native crystals and from identical crystals soaked in a solution containing potassium cyanide. In both structures, the substrate H(2)O/OH(-) molecule exhibits binding to the unique Fe site of the C-cluster. We also observe cyanide binding in a bent conformation to Ni of the C-cluster, adjacent the substrate H(2)O/OH(-) molecule. Importantly, the bridging sulfide is not present in either structure. As these forms of the C-cluster represent the coordination environment immediately before the reaction takes place, our findings do not support a fifth, bridging sulfide playing a catalytic role in the enzyme mechanism. The crystal structures presented here, along with recent structures of CODHs from other organisms, have led us toward a unified mechanism for CO oxidation by the C-cluster, the catalytic center of an environmentally important enzyme.

PubMed: 19583207
DOI: 10.1021/bi900574h

Experimental method

X-RAY DIFFRACTION (2.15 Å)