3VI0

Crystal structure of the O intermediate of the L93A mutant of bacteriorhodopsin

Summary for 3VI0

• Entry DOI: 10.2210/pdb3vi0/pdb
• Related: 3vhz
• Descriptor: Bacteriorhodopsin, 3-O-sulfo-beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose, RETINAL, ... (6 entities in total)
• Functional Keywords: retinal protein, seven transmembrane helices, light-driven proton pump, cell membrane, proton transport
• Biological source: Halobacterium
• Cellular location: Cell membrane; Multi-pass membrane protein: P02945
• Total number of polymer chains: 1
• Total formula weight: 30058.53

Authors

Kouyama, T.,Zhang, J. (deposition date: 2011-09-13, release date: 2012-06-13, Last modification date: 2024-10-16)

Primary citation

Zhang, J.,Yamazaki, Y.,Hikake, M.,Murakami, M.,Ihara, K.,Kouyama, T.
Crystal structure of the O intermediate of the Leu93Ala mutant of bacteriorhodopsin
Proteins, 80:2384-2396, 2012

PubMed Abstract: The lifetime of the O intermediate of bacteriorhodopsin (BR) is extended by a factor of ∼250 in the Leu93-to-Ala mutant (BR_L93A). To clarify the structural changes occurring in the last stage of the proton pumping cycle of BR, we crystallized BR_L93A into a hexagonal P622 crystal. Diffraction data from the unphotolyzed state showed that the deletion of three carbon atoms from Leu93 is compensated by the insertion of four water molecules in the cytoplasmic vicinity of retinal. This insertion of water is suggested to be responsible for the blue-shifted λ(max) (540 nm) of the mutant. A long-lived substate of O with a red-shifted λ(max) (~565 nm) was trapped when the crystal of BR_L93A was flash-cooled after illumination with green light. This substate (O(slow)) bears considerable similarity to the M intermediate of native BR; that is, it commonly shows deformation of helix C and the FG loop, downward orientation of the side chain of Arg82, and disruption of the Glu194/Glu204 pair. In O(slow), however, the main chain of Lys216 is less distorted and retinal takes on the 13-cis/15-syn configuration. Another significant difference is seen in the pH dependence of the structure of the proton release group, the pK(a) value of which is suggested to be much lower in O(slow) than in M.

PubMed: 22641602
DOI: 10.1002/prot.24124

Experimental method

X-RAY DIFFRACTION (2.3 Å)