2Z8Y

Xenon-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase(CODH/ACS) from Moorella thermoacetica

Summary for 2Z8Y

• Entry DOI: 10.2210/pdb2z8y/pdb
• Related: 1MJG
• Descriptor: Carbon monoxide dehydrogenase/acetyl CoA synthase subunit beta, Carbon monoxide dehydrogenase/acetyl CoA synthase subunit alpha, IRON/SULFUR CLUSTER, ... (9 entities in total)
• Functional Keywords: xenon, carbon monoxide (co) channel, nickel-iron-sulfur (ni-fe-s) cluster, nickel-copper-iron-sulfur (ni-cu-fe-s) cluster, helical domain, rossmann fold, clostridium thermoaceticum, wood-ljundahl pathway, carbon dioxide fixation, electron transport, metal-binding, oxidoreductase, transport, transferase, oxidoreductase-transferase complex, oxidoreductase/transferase
• Biological source: Moorella thermoacetica; More
• Total number of polymer chains: 8
• Total formula weight: 630944.30

Authors

Doukov, T.I.,Blasiak, L.C.,Drennan, C.L. (deposition date: 2007-09-12, release date: 2008-03-11, Last modification date: 2023-11-01)

Primary citation

Doukov, T.I.,Blasiak, L.C.,Seravalli, J.,Ragsdale, S.W.,Drennan, C.L.
Xenon in and at the End of the Tunnel of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase
Biochemistry, 47:3474-3483, 2008

PubMed Abstract: A fascinating feature of some bifunctional enzymes is the presence of an internal channel or tunnel to connect the multiple active sites. A channel can allow for a reaction intermediate generated at one active site to be used as a substrate at a second active site, without the need for the intermediate to leave the safety of the protein matrix. One such bifunctional enzyme is carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica (mtCODH/ACS). A key player in the global carbon cycle, CODH/ACS uses a Ni-Fe-S center called the C-cluster to reduce carbon dioxide to carbon monoxide and uses a second Ni-Fe-S center, called the A-cluster, to assemble acetyl-CoA from a methyl group, coenzyme A, and C-cluster-generated CO. mtCODH/ACS has been proposed to contain one of the longest enzyme channels (138 A long) to allow for intermolecular CO transport. Here, we report a 2.5 A resolution structure of xenon-pressurized mtCODH/ACS and examine the nature of gaseous cavities within this enzyme. We find that the cavity calculation program CAVENV accurately predicts the channels connecting the C- and A-clusters, with 17 of 19 xenon binding sites within the predicted regions. Using this X-ray data, we analyze the amino acid composition surrounding the 19 Xe sites and consider how the protein fold is utilized to carve out such an impressive interior passageway. Finally, structural comparisons of Xe-pressurized mtCODH/ACS with related enzyme structures allow us to study channel design principles, as well as consider the conformational flexibility of an enzyme that contains a cavity through its center.

PubMed: 18293927
DOI: 10.1021/bi702386t

Experimental method

X-RAY DIFFRACTION (2.51 Å)