1DZE

Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K

Summary for 1DZE

• Entry DOI: 10.2210/pdb1dze/pdb
• Related: 1AP9 1AT9 1BAC 1BAD 1BCT 1BHA 1BHB 1BRD 1BRR 1C3W 1QM8 2BRD
• Descriptor: BACTERIORHODOPSIN (M INTERMEDIATE), beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose, RETINAL, ... (8 entities in total)
• Functional Keywords: bacteriorhodopsin, proton pump, membrane protein, retinal protein, photoreceptor, reaction intermediate, halobacteria, ion pump, helix, sliding
• Biological source: HALOBACTERIUM SALINARIUM
• Total number of polymer chains: 1
• Total formula weight: 31335.13

Authors

Takeda, K.,Matsui, Y.,Sato, H.,Hino, T.,Kanamori, E.,Okumura, H.,Yamane, T.,Iizuka, T.,Kamiya, N.,Adachi, S.,Kouyama, T. (deposition date: 2000-02-25, release date: 2000-08-16, Last modification date: 2024-10-23)

Primary citation

Takeda, K.,Matsui, Y.,Kamiya, N.,Adachi, S.,Okumura, H.,Kouyama, T.
Crystal Structure of the M Intermediate of Bacteriorhodopsin: Allosteric Structural Changes Mediated by Sliding Movement of a Transmembrane Helix
J.Mol.Biol., 341:1023-, 2004

PubMed Abstract: Structural changes in the proton pumping cycle of wild-type bacteriorhodopsin were investigated by using a 3D crystal (space group P622)prepared by the membrane fusion method. Protein-protein contacts in the crystal elongate the lifetime of the M intermediate by a factor of approximately 100,allowing high levels of the M intermediate to accumulate under continuous illumination. When the M intermediate generated at room temperature was exposed to a low flux of X-rays (approximately 10(14) photons/mm2), this yellow intermediate was converted into a blue species having an absorption maximum at 650 nm. This color change is suggested to accompany a configuration change in the retinal-Lys216 chain. The true conformational change associated with formation of the M intermediate was analyzed by taking the X-radiation-induced structural change into account. Our result indicates that, upon formation of the M intermediate, helix G move stowards the extra-cellular side by, on average, 0.5 angstroms. This movement is coupled with several reactions occurring at distal sites in the protein: (1) reorientation of the side-chain of Leu93 contacting the C13 methyl group of retinal, which is accompanied by detachment of a water molecule from the Schiff base; (2) a significant distortion in the F-G loop, triggering destruction of a hydrogen bonding interaction between a pair of glutamate groups (Glu194 and Glu204); (3) formation of a salt bridge between the carboxylate group of Glu204 and the guanidinium ion of Arg82, which is accompanied by a large distortion in the extra-cellular half of helix C; (4)noticeable movements of the AB loop and the cytoplasmic end of helix B. But, no appreciable change is induced in the peptide backbone of helices A,D, E and F. These structural changes are discussed from the viewpoint of translocation of water molecules.

PubMed: 15328615
DOI: 10.1016/J.JMB.2004.06.080

Experimental method

X-RAY DIFFRACTION (2.5 Å)