7W74

Crystal structure of DTG rhodopsin from Pseudomonas putida

Summary for 7W74

• Entry DOI: 10.2210/pdb7w74/pdb
• Descriptor: Bacteriorhodopsin-like protein, RETINAL, (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, ... (5 entities in total)
• Functional Keywords: light-driven proton pump, seven transmembrane helices, retinal, dtg motif, membrane protein
• Biological source: Pseudomonas putida
• Total number of polymer chains: 2
• Total formula weight: 55069.80

Authors

Suzuki, K.,Konno, M.,Bagherzadeh, R.,Inoue, K.,Murata, T. (deposition date: 2021-12-03, release date: 2022-02-23, Last modification date: 2024-11-20)

Primary citation

Suzuki, K.,Del Carmen Marin, M.,Konno, M.,Bagherzadeh, R.,Murata, T.,Inoue, K.
Structural characterization of proton-pumping rhodopsin lacking a cytoplasmic proton donor residue by X-ray crystallography.
J.Biol.Chem., 298:101722-101722, 2022

PubMed Abstract: DTG/DTS rhodopsin, which was named based on a three-residue motif (DTG or DTS) that is important for its function, is a light-driven proton-pumping microbial rhodopsin using a retinal chromophore. In contrast to other light-driven ion-pumping rhodopsins, DTG/DTS rhodopsin does not have a cytoplasmic proton donor residue, such as Asp, Glu, or Lys. Because of the lack of cytoplasmic proton donor residue, proton directly binds to the retinal chromophore from the cytoplasmic solvent. However, mutational experiments that showed the complicated effects of mutations were not able to clarify the roles played by each residue, and the detail of proton uptake pathway is unclear because of the lack of structural information. To understand the proton transport mechanism of DTG/DTS rhodopsin, here we report the three-dimensional structure of one of the DTG/DTS rhodopsins, PspR from Pseudomonas putida, by X-ray crystallography. We show that the structure of the cytoplasmic side of the protein is significantly different from that of bacteriorhodopsin, the best-characterized proton-pumping rhodopsin, and large cytoplasmic cavities were observed. We propose that these hydrophilic cytoplasmic cavities enable direct proton uptake from the cytoplasmic solvent without the need for a specialized cytoplasmic donor residue. The introduction of carboxylic residues homologous to the cytoplasmic donors in other proton-pumping rhodopsins resulted in higher pumping activity with less pH dependence, suggesting that DTG/DTS rhodopsins are advantageous for producing energy and avoiding intracellular alkalization in soil and plant-associated bacteria.

PubMed: 35151692
DOI: 10.1016/j.jbc.2022.101722

Experimental method

X-RAY DIFFRACTION (2.84 Å)