One-carbon chemistry of oxalate oxidoreductase captured by X-ray crystallography

Marcus I. Gibson; Percival Yang-Ting Chen; Aileen C. Johnson; Elizabeth Pierce; Mehmet Can; Stephen W. Ragsdale; Catherine L. Drennan

doi:10.1073/pnas.1518537113

New Research In

Edited by Gregory A. Petsko, Weill Cornell Medical College, New York, NY, and approved November 30, 2015 (received for review September 21, 2015)

Significance

The microbial Wood−Ljungdahl pathway is the biological equivalent of the Monsanto process, responsible for converting greenhouse gas CO₂ into acetate. In addition to CO₂, this microbial pathway requires low-potential electrons. The recently discovered oxalate oxidoreductase produces both low-potential electrons and CO₂ through the oxidation of oxalate. Here our structural data allow us to visualize intermediates along the reaction cycle that have not been previously described, providing insight into the molecular mechanism by which oxalate is metabolized.

Abstract

Thiamine pyrophosphate (TPP)-dependent oxalate oxidoreductase (OOR) metabolizes oxalate, generating two molecules of CO₂ and two low-potential electrons, thus providing both the carbon and reducing equivalents for operation of the Wood−Ljungdahl pathway of acetogenesis. Here we present structures of OOR in which two different reaction intermediate bound states have been trapped: the covalent adducts between TPP and oxalate and between TPP and CO₂. These structures, along with the previously determined structure of substrate-free OOR, allow us to visualize how active site rearrangements can drive catalysis. Our results suggest that OOR operates via a bait-and-switch mechanism, attracting substrate into the active site through the presence of positively charged and polar residues, and then altering the electrostatic environment through loop and side chain movements to drive catalysis. This simple but elegant mechanism explains how oxalate, a molecule that humans and most animals cannot break down, can be used for growth by acetogenic bacteria.

Footnotes

↵¹Present address: Department of Chemistry, Princeton University, Princeton, NJ 08540.
↵²Present address: Emory University School of Medicine, Atlanta, GA 30307.
↵³Present address: Physical Science Department, Southern Utah University, Cedar City, UT 84720.
↵⁴To whom correspondence should be addressed. Email: cdrennan{at}mit.edu.

Author contributions: M.I.G., S.W.R., and C.L.D. designed research; M.I.G., P.Y.-T.C., A.C.J., E.P., and M.C. performed research; M.I.G., P.Y.-T.C., S.W.R., and C.L.D. analyzed data; and M.I.G. and C.L.D. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The atomic coordinates have been deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 5EXD and 5EXE).
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1518537113/-/DCSupplemental.

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