5B0W

Crystal structure of the 11-cis isomer of pharaonis halorhodopsin in the absence of halide ions

Summary for 5B0W

• Entry DOI: 10.2210/pdb5b0w/pdb
• Related: 3qbg
• Descriptor: Halorhodopsin, RETINAL, BACTERIORUBERIN, ... (7 entities in total)
• Functional Keywords: seven trans-membrane helices, retinylidene protein, light-driven chloride ion pump microbial rhodopsin, membrane protein
• Biological source: Natronomonas pharaonis DSM 2160
• Total number of polymer chains: 6
• Total formula weight: 195885.34

Authors

Kouyama, T.,Chan, S.K. (deposition date: 2015-11-11, release date: 2016-07-27, Last modification date: 2020-07-29)

Primary citation

Chan, S.K.,Kawaguchi, H.,Kubo, H.,Murakami, M.,Ihara, K.,Maki, K.,Kouyama, T.
Crystal Structure of the 11-cis Isomer of Pharaonis Halorhodopsin: Structural Constraints on Interconversions among Different Isomeric States
Biochemistry, 55:4092-4104, 2016

PubMed Abstract: Like other microbial rhodopsins, the light driven chloride pump halorhodopsin from Natronomonas pharaonis (pHR) contains a mixture of all-trans/15-anti and 13-cis/15-syn isomers in the dark adapted state. A recent crystallographic study of the reaction states of pHR has shown that reaction states with 13-cis/15-syn retinal occur in the anion pumping cycle that is initiated by excitation of the all-trans isomer. In this study, we investigated interconversions among different isomeric states of pHR in the absence of chloride ions. The illumination of chloride free pHR with red light caused a large blue shift in the absorption maximum of the retinal visible band. During this "red adaptation", the content of the 11-cis isomer increased significantly, while the molar ratio of the 13-cis isomer to the all-trans isomer remained unchanged. The results suggest that the thermally activated interconversion between the 13-cis and the all-trans isomers is very rapid. Diffraction data from red adapted crystals showed that accommodation of the retinal chromophore with the 11-cis/15-syn configuration was achieved without a large change in the retinal binding pocket. The measurement of absorption kinetics under illumination showed that the 11-cis isomer, with a λmax at 565 nm, was generated upon excitation of a red-shifted species (λmax = 625 nm) that was present as a minor component in the dark adapted state. It is possible that this red-shifted species mimics an O-like reaction state with 13-cis/15-syn retinal, which was hypothesized to occur at a late stage of the anion pumping cycle.

PubMed: 27352034
DOI: 10.1021/acs.biochem.6b00277

Experimental method

X-RAY DIFFRACTION (1.7 Å)