2ZZL

Structure of bacteriorhodopsin's M intermediate at pH 7

Summary for 2ZZL

• Entry DOI: 10.2210/pdb2zzl/pdb
• Related: 1iw6 1iw9
• Descriptor: Bacteriorhodopsin, 3-O-sulfo-beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose, RETINAL, ... (8 entities in total)
• Functional Keywords: retinal, protein-lipid complex, reaction intermediate, cell membrane, chromophore, hydrogen ion transport, ion transport, membrane, photoreceptor protein, pyrrolidone carboxylic acid, receptor, retinal protein, sensory transduction, transmembrane, transport, proton transport
• Biological source: Halobacterium salinarum
• Cellular location: Cell membrane; Multi-pass membrane protein: P02945
• Total number of polymer chains: 1
• Total formula weight: 33185.20

Authors

Yamamoto, M.,Kouyama, T. (deposition date: 2009-02-18, release date: 2009-10-06, Last modification date: 2023-11-01)

Primary citation

Yamamoto, M.,Hayakawa, N.,Murakami, M.,Kouyama, T.
Crystal Structures of Different Substates of Bacteriorhodopsin's M Intermediate at Various pH Levels.
J.Mol.Biol., 2009

PubMed Abstract: The hexagonal P622 crystal of bacteriorhodopsin, which is made up of stacked membranes, is stable provided that the precipitant concentration in the soaking solution is higher than a critical value (i.e., 1.5 M ammonium sulfate). Diffraction data showed that the crystal lattice shrank linearly with increasing precipitant concentration, due primarily to narrowing of intermembrane spaces. Although the crystal shrinkage did not affect the rate of formation of the photoreaction M intermediate, its lifetime increased exponentially with the precipitant concentration. It was suggested that the energetic barrier of the M-to-N transition becomes higher when the motional freedom of the EF loop is reduced by crystal lattice force. As a result of this property, the M state accumulated predominantly when the crystal that was soaked at a high precipitant concentration was illuminated at room temperature. Structural data obtained at various pH levels showed that the overall structure of M is not strongly dependent on pH, except that Glu194 and Glu204 in the proton release complex are more separated at pH 7 than at pH 4.4. This result suggests that light-induced disruption of the paired structure of Glu194 and Glu204 is incomplete when external pH is lower than the pK(a) value of the proton release group in the M state.

PubMed: 19712684
DOI: 10.1016/j.jmb.2009.08.047

Experimental method

X-RAY DIFFRACTION (2.03 Å)