1UCQ

Crystal structure of the L intermediate of bacteriorhodopsin

Summary for 1UCQ

• Entry DOI: 10.2210/pdb1ucq/pdb
• Related: 1iw6 1iw9 1ixf
• Descriptor: bacteriorhodopsin, beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose, RETINAL, ... (6 entities in total)
• Functional Keywords: proton pump, retinal protein, membrane protein, protein-lipid complex, reaction intermediate, proton transport
• Biological source: Halobacterium salinarum
• Cellular location: Cell membrane; Multi-pass membrane protein: P02945
• Total number of polymer chains: 1
• Total formula weight: 31912.25

Authors

Kouyama, T.,Nishikawa, T.,Tokuhisa, T.,Okumura, H. (deposition date: 2003-04-17, release date: 2003-12-30, Last modification date: 2024-10-30)

Primary citation

Kouyama, T.,Nishikawa, T.,Tokuhisa, T.,Okumura, H.
Crystal Structure of the L Intermediate of Bacteriorhodopsin: Evidence for Vertical Translocation of a Water Molecule during the Proton Pumping Cycle.
J.Mol.Biol., 335:531-546, 2004

PubMed Abstract: For structural investigation of the L intermediate of bacteriorhodopsin, a 3D crystal belonging to the space group P622 was illuminated with green light at 160 K and subsequently with red light at 100 K. This yielded a approximately 1:4 mixture of the L intermediate and the ground-state. Diffraction data from such crystals were collected using a low flux of X-rays ( approximately 2 x 10(15) photons/mm2 per crystal), and their merged data were compared with those from unphotolyzed crystals. These structural data, together with our previous data, indicate that the retinal chromophore, which is largely twisted in the K-intermediate, takes a more planar 13-cis, 15-anti configuration in the L intermediate. This configurational change, which is accompanied by re-orientation of the Schiff base N-H bond towards the intracellular side, is coupled with a large rotation of the side-chain of an amino acid residue (Leu93) making contact with the C13 methyl group of retinal. Following these motions, a water molecule, at first hydrogen-bonded to the Schiff base and Asp85, is dragged to a space that is originally occupied by Leu93. Diffraction data from a crystal containing the M intermediate showed that this water molecule moves further towards the intracellular side in the L-to-M transition. It is very likely that detachment of this water molecule from the protonated Schiff base causes a significant decrease in the pKa of the Schiff base, thereby facilitating the proton transfer to Asp85. On the basis of these observations, we argue that the vertical movement of a water molecule in the K-to-L transition is a key event determining the directionality of proton translocation in the protein.

PubMed: 14672661
DOI: 10.1016/j.jmb.2003.10.068

Experimental method

X-RAY DIFFRACTION (2.4 Å)