6kfq

Crystal structure of thermophilic rhodopsin from Rubrobacter xylanophilus

spinqualitylabelsall models 6kfq, resolution 1.84Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6kfq is a 1 chain structure with sequence from Rubrobacter xylanophilus DSM 9941. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.84Å Ligands: MPG, RET, SO4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q1AUE6_RUBXD Publication Abstract from PubMed We often encounter a case where two proteins, whose amino-acid sequences are similar, are quite different with regard to the thermostability. As a striking example, we consider the two seven-transmembrane proteins: recently discovered Rubrobacter xylanophilus rhodopsin (RxR) and long-known bacteriorhodopsin from Halobacterium salinarum (HsBR). They commonly function as a light-driven proton pump across the membrane. Though their sequence similarity and identity are approximately 71 and approximately 45%, respectively, RxR is much more thermostable than HsBR. In this study, we solve the three-dimensional structure of RxR using X-ray crystallography and find that the backbone structures of RxR and HsBR are surprisingly similar to each other: The root-mean-square deviation for the two structures calculated using the backbone Calpha atoms of the seven helices is only 0.86 A, which makes the large stability difference more puzzling. We calculate the thermostability measure and its energetic and entropic components for RxR and HsBR using our recently developed statistical-mechanical theory. The same type of calculation is independently performed for the portions playing essential roles in the proton-pumping function, helices 3 and 7, and their structural properties are related to the probable roles of water molecules in the proton-transporting mechanism. We succeed in elucidating how RxR realizes its exceptionally high stability with the original function being retained. This study provides an important first step toward the establishment of a method correlating microscopic, geometric characteristics of a protein with its thermodynamic properties and enhancing the thermostability through amino-acid mutations without vitiating the original function. How Does a Microbial Rhodopsin RxR Realize Its Exceptionally High Thermostability with the Proton-Pumping Function Being Retained?,Hayashi T, Yasuda S, Suzuki K, Akiyama T, Kanehara K, Kojima K, Tanabe M, Kato R, Senda T, Sudo Y, Murata T, Kinoshita M J Phys Chem B. 2020 Feb 13;124(6):990-1000. doi: 10.1021/acs.jpcb.9b10700. Epub, 2020 Feb 3. PMID:31955569 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Rhodopsin 3D structures

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