7XJD

Crystal structure of bacteriorhodopsin in the ground state by red laser irradiation

Summary for 7XJD

• Entry DOI: 10.2210/pdb7xjd/pdb
• Related: 7XJC 7XJE
• Descriptor: Bacteriorhodopsin, RETINAL, 2,3-DI-PHYTANYL-GLYCEROL, ... (5 entities in total)
• Functional Keywords: proton pump, membrane protein, proton transport
• Biological source: Halobacterium salinarum NRC-1
• Total number of polymer chains: 1
• Total formula weight: 36142.30

Authors

Taguchi, S.,Niwa, S.,Takeda, K. (deposition date: 2022-04-16, release date: 2023-03-22, Last modification date: 2025-06-18)

Primary citation

Taguchi, S.,Niwa, S.,Dao, H.A.,Tanaka, Y.,Takeda, R.,Fukai, S.,Hasegawa, K.,Takeda, K.
Detailed analysis of distorted retinal and its interaction with surrounding residues in the K intermediate of bacteriorhodopsin.
Commun Biol, 6:190-190, 2023

PubMed Abstract: The K intermediate of proton pumping bacteriorhodopsin is the first intermediate generated after isomerization of retinal to the 13-cis form. Although various structures have been reported for the K intermediate until now, these differ from each other, especially in terms of the conformation of the retinal chromophore and its interaction with surrounding residues. We report here an accurate X-ray crystallographic analysis of the K structure. The polyene chain of 13-cis retinal is observed to be S-shaped. The side chain of Lys216, which is covalently bound to retinal via the Schiff-base linkage, interacts with residues, Asp85 and Thr89. In addition, the Nζ-H of the protonated Schiff-base linkage interacts with a residue, Asp212 and a water molecule, W402. Based on quantum chemical calculations for this K structure, we examine the stabilizing factors of distorted conformation of retinal and propose a relaxation manner to the next L intermediate.

PubMed: 36808185
DOI: 10.1038/s42003-023-04554-2

Experimental method

X-RAY DIFFRACTION (1.33 Å)