Researchers suggest that a pipeline to cut agricultural emissions could be combined with soil carbon sequestration to achieve net negative emissions in row crop agriculture.
Image credit: Pixabay/trueckauer.
Edited by Harry B. Gray, California Institute of Technology, Pasadena, CA, and approved July 14, 2021 (received for review April 11, 2021)
Significance
Quinol oxidases that are members of the heme–copper superfamily of respiratory oxygen reductases have evolved from cytochrome c oxidases. They directly oxidize quinol and reduce oxygen to water. Here, we describe two high-resolution cryogenic electron microscopy structures of the proton-pumping cytochrome bo3 ubiquinol oxidase in styrene–maleic acid copolymer nanodiscs and in membrane scaffold protein nanodiscs. Each structure contains one equivalent of well-resolved ubiquinone-8 in the substrate binding site as well as several phospholipid molecules. These structures indicate that H98I has two conformations that allow H98I hydrogen bonded to carbonyl O4 of the UQ8 or with E14I. We propose that H98I dynamics serves to shuttle protons from ubiquinol-8 via E14I to the bulk aqueous phase upon ubiquinol-8 oxidation.
Abstract
Two independent structures of the proton-pumping, respiratory cytochrome bo3 ubiquinol oxidase (cyt bo3) have been determined by cryogenic electron microscopy (cryo-EM) in styrene–maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme b, heme o3, and CuB), the redox-active cross-linked histidine–tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome c oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75I and R71I. In both structures, residue H98I occupies two conformations. In conformation 1, H98I forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98I has flipped to form a hydrogen bond with E14I at the N-terminal end of TM0. We propose that H98I dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98I.
Footnotes
↵1J.L., L.H., and F.V. contributed equally to this work.
- ↵2To whom correspondence may be addressed. Email: r-gennis{at}illinois.edu, jack.zhang{at}yale.edu, oc2188{at}cumc.columbia.edu, or zhujiapeng{at}hotmail.com.
Author contributions: J.L., J.Z., O.C., K.Z., and R.G. designed research; J.L., L.H., F.V., Y.L., C.K.C., E.T., and K.Z. performed research; Z.D., S.K.C., S.H., Y.L., J.Z., O.C., and R.G. analyzed data; and J.L., F.V., Z.D., S.K.C., B.L., C.K.C., E.T., J.Z., O.C., K.Z., and R.G. wrote the paper.
The authors declare no competing interest.
This article is a PNAS Direct Submission.
This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2106750118/-/DCSupplemental.
Data Availability
Protein structure coordinates and maps data have been deposited in Protein Data Bank https://www.rcsb.org/ (7CUB, 7CUW, 7CUQ, and 7N9Z) and Electron Microscopy Databank https://www.ebi.ac.uk/emdb/ (EMD-30471, EMD-30475, EMD-30474, EMD-30817, EMD-30819, EMD-30818, and EMD-24265). The data will be accessible upon publication. All other study data are included in the article and/or SI Appendix.
Published under the PNAS license.
References
Log in using your username and password
Log in through your institution
You may be able to gain access using your login credentials for your institution. Contact your library if you do not have a username and password.
If your organization uses OpenAthens, you can log in using your OpenAthens username and password. To check if your institution is supported, please see this list. Contact your library for more details.
Purchase access
You may purchase access to this article. This will require you to create an account if you don't already have one.
Cryo-EM structures of Escherichia coli cytochrome bo3 reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site
Article Classifications
- Biological Sciences
- Biochemistry
- Physical Sciences
- Chemistry
Sign up for Article Alerts
Jump to section
You May Also be Interested in
Features on Venus suggest limited yet global crustal deformation driven by a convecting planetary interior.
Image credit: Paul K. Byrne and Sean C. Solomon.
A study estimates that the sum of all SARS-CoV-2 virions found in human hosts may weigh between 100 grams and 10 kilograms.
Image credit: Pixabay/thiagolazarino.
Recently discovered cave paintings and bone carvings offer new perspectives on long-held questions about art’s origins—not to mention the nature of art itself.
Image credit: Maxime Aubert (Griffith University, Nathan QLD, Australia).
The current system may make it hard for new ideas to unseat dominant, older ones.
Image credit: Shutterstock/Sergei25.