Structural and functional characterization of an otopetrin family proton channel

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Abstract

The otopetrin (OTOP) proteins were recently characterized as proton channels. Here we present the cryo-EM structure of OTOP3 from Xenopus tropicalis (XtOTOP3) along with functional characterization of the channel. XtOTOP3 forms a homodimer with each subunit containing 12 transmembrane helices that can be divided into two structurally homologous halves; each half assembles as an α-helical barrel that could potentially serve as a proton conduction pore. Both pores open from the extracellular half before becoming occluded at a central constriction point consisting of three highly conserved residues - Gln_232/585-Asp₂₆₂/Asn₆₂₃-Tyr_322/666 (the constriction triads). Mutagenesis shows that the constriction triad from the second pore is less amenable to perturbation than that of the first pore, suggesting an unequal contribution between the two pores to proton transport. We also identified several key residues at the interface between the two pores that are functionally important, particularly Asp509, which confers intracellular pH-dependent desensitization to OTOP channels.

Data availability

The cryo-EM density map of the XtOTOP3 has been deposited in the Electron Microscopy Data Bank under accession numbers EMDB-0650. Atomic coordinate has been deposited in the Protein Data Bank under accession number 6O84.

The following data sets were generated

1. Chen Q
2. Bai X-c
3. Jiang Y
(2019) Cryo-EM density map of OTOP3 from xenopus tropicalis
Electron Microscopy Data Bank, EMD-0650.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-0650
1. Chen Q
2. Bai X-c
3. Jiang Y
(2019) Atomic coordinates of OTOP3 from xenopus tropicalis
Protein Data Bank, 6O84.

http://www.rcsb.org/structure/6O84

Article and author information

Author details

Qingfeng Chen

Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States

Competing interests
The authors declare that no competing interests exist.
Weizhong Zeng

Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States

Competing interests
The authors declare that no competing interests exist.
Ji She

Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-7006-6230
Xiaochen Bai

Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States

For correspondence
Xiaochen.Bai@UTSouthwestern.edu

Competing interests
The authors declare that no competing interests exist.
Youxing Jiang

Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States

For correspondence
youxing.jiang@utsouthwestern.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-1874-0504

Funding

National Institute of General Medical Sciences (GM079179)

Youxing Jiang

Howard Hughes Medical Institute

Youxing Jiang

Welch Foundation (I-1578)

Youxing Jiang

Cancer Prevention and Research Institute of Texas

Xiaochen Bai

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.