7XJD

Detailed analysis of distorted retinal and its interaction with surrounding residues in the K intermediate of bacteriorhodopsin.

(2023) Commun Biol 6: 190-190

• PubMed: 36808185 Search on PubMedSearch on PubMed Central
• DOI: https://doi.org/10.1038/s42003-023-04554-2
• Primary Citation of Related Structures:  
  7XJD


• 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 ...

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.

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Organizational Affiliation: 

Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Sakyo-ku, 606-8502, Japan. ktakeda@kuchem.kyoto-u.ac.jp.


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