Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore

Abstract

Homologous to bacteriorhodopsin and even more to proteorhodopsin, xanthorhodopsin is a light-driven proton pump that, in addition to retinal, contains a noncovalently bound carotenoid with a function of a light-harvesting antenna. We determined the structure of this eubacterial membrane protein-carotenoid complex by X-ray diffraction, to 1.9-Å resolution. Although it contains 7 transmembrane helices like bacteriorhodopsin and archaerhodopsin, the structure of xanthorhodopsin is considerably different from the 2 archaeal proteins. The crystallographic model for this rhodopsin introduces structural motifs for proton transfer during the reaction cycle, particularly for proton release, that are dramatically different from those in other retinal-based transmembrane pumps. Further, it contains a histidine-aspartate complex for regulating the pK a of the primary proton acceptor not present in archaeal pumps but apparently conserved in eubacterial pumps. In addition to aiding elucidation of a more general proton transfer mechanism for light-driven energy transducers, the structure defines also the geometry of the carotenoid and the retinal. The close approach of the 2 polyenes at their ring ends explains why the efficiency of the excited-state energy transfer is as high as Ϸ45%, and the 46°angle between them suggests that the chromophore location is a compromise between optimal capture of light of all polarization angles and excited-state energy transfer.carotenoid antenna ͉ energy transfer ͉ retinal protein ͉ salinixanthin ͉ X-ray structure

Structural insights into the proton pumping by unusual proteorhodopsin from nonmarine bacteria

“…This arrangement stabilizes the positive charge of the Schiff base and is conserved in all of the currently known proton pumps (and in most other retinylidene proteins). The carboxylate of Asp-85 in ESR is oriented in a similar way to Asp-85 of BR and unlike its homolog Asp-96 in xanthorhodopsin, which is considerably rotated (12). One more water molecule, W406, is observed in the retinal binding pocket of ESR, where it occupies a similar position to W406 of BR (Figs.…”

“…Whereas, in BR, W406 forms a hydrogen bond to Arg-82 (22,23), in ESR, it is close to other water molecules directly facing the bulk solvent. In the structure of xanthorhodopsin, only the water molecule W402 was found (12).…”

“…The keto-ring of salinixanthin interacts with the residues at the extracellular ends of the helices E and F and the β-ionone ring of the retinal. The binding pocket of the keto-ring is formed by Leu-148, Gly-156, Phe-157, Thr-160, Met-208, and Met-211 and the retinal β-ionone ring (12). An intriguing question is whether other retinal proteins might also have an antenna.…”

“…Here, we present a high-resolution crystallographic structure of ESR and show that it is very unusual compared with the structures of BR and xanthorhodopsin (XR) (12), the closest ESR homolog and the only proton-pumping bacterial rhodopsin for which the crystallographic structure is known. We show that the ESR structure possesses a proteorhodopsin-specific feature and may serve as a model for the protein family.…”

“…However, it was shown recently that a light-harvesting antenna can function also in a retinal protein. Xanthorhodopsin, a retinylidene protein of the extreme halophilic bacterium Salinibacter ruber isolated from salt-crystallizer ponds, contains a single energy-donor carotenoid, salinixanthin, as an additional chromophore (12,21). The salinixanthin binds to the outer surface of the helix F at the protein-lipid boundary.…”