Structure of the α2ε2 Ni-dependent CO dehydrogenase component of the Methanosarcina barkeri acetyl-CoA decarbonylase/synthase complex

doi:10.1073/pnas.0800415105

Structure of the α₂ε₂ Ni-dependent CO dehydrogenase component of the Methanosarcina barkeri acetyl-CoA decarbonylase/synthase complex

Departments of ^¶Biochemistry,
^§§Chemistry and
^‖Microbiology, and
^††Ohio State Biochemistry Program, Ohio State University, 484 West 12th Avenue, Columbus, OH 43210;
^†National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China; and
^‡School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China

Edited by Harry B. Gray, California Institute of Technology, Pasadena, CA, and approved April 21, 2008
↵^§W.G. and B.H. contributed equally to this work. (received for review January 15, 2008)

Abstract

Ni-dependent carbon monoxide dehydrogenases (Ni-CODHs) are a diverse family of enzymes that catalyze reversible CO:CO₂ oxidoreductase activity in acetogens, methanogens, and some CO-using bacteria. Crystallography of Ni-CODHs from CO-using bacteria and acetogens has revealed the overall fold of the Ni-CODH core and has suggested structures for the C cluster that mediates CO:CO₂ interconversion. Despite these advances, the mechanism of CO oxidation has remained elusive. Herein, we report the structure of a distinct class of Ni-CODH from methanogenic archaea: the α₂ε₂ component from the α₈β₈γ₈δ₈ε₈ CODH/acetyl-CoA decarbonylase/synthase complex, an enzyme responsible for the majority of biogenic methane production on Earth. The structure of this Ni-CODH component provides support for a hitherto unobserved state in which both CO and H₂O/OH^- bind to the Ni and the exogenous FCII iron of the C cluster, respectively, and offers insight into the structures and functional roles of the ε-subunit and FeS domain not present in nonmethanogenic Ni-CODHs.

Footnotes

^‡‡To whom correspondence may be addressed. E-mail: krzycki.1{at}osu.edu or chan{at}chemistry.ohio-state.edu
Author contributions: B.H., J.A.K., and M.K.C. designed research; W.G., B.H., Z.W., D.J.F., T.T., and M.K.C. performed research; W.G., B.H., Z.W., J.A.K., and M.K.C. analyzed data; and W.G., B.H., J.A.K., and M.K.C. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The coordinates have been deposited in the Protein Data Bank (PDB ID code 3CF4).
This article contains supporting information online at www.pnas.org/cgi/content/full/0800415105/DCSupplemental.