1IXF

Crystal Structure of the K intermediate of bacteriorhodopsin

Summary for 1IXF

• Entry DOI: 10.2210/pdb1ixf/pdb
• Related: 1iw6 1iw9
• Descriptor: bacteriorhodopsin, beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose, RETINAL, ... (6 entities in total)
• Functional Keywords: 7-helices, 13-cis retinal, riken structural genomics/proteomics initiative, rsgi, structural genomics, proton transport
• Biological source: Halobacterium salinarum
• Cellular location: Cell membrane; Multi-pass membrane protein: P02945
• Total number of polymer chains: 1
• Total formula weight: 31797.16

Authors

Matsui, Y.,Sakai, K.,Murakami, M.,Shiro, Y.,Adachi, S.,Okumura, H.,Kouyama, T.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2002-06-20, release date: 2002-12-18, Last modification date: 2024-10-09)

Primary citation

Matsui, Y.,Sakai, K.,Murakami, M.,Shiro, Y.,Adachi, S.,Okumura, H.,Kouyama, T.
Specific Damage Induced by X-ray Radiation and Structural Changes in the Primary Photoreaction of Bacteriorhodopsin
J.MOL.BIOL., 324:469-481, 2002

PubMed Abstract: Bacteriorhodopsin, the sole membrane protein of the purple membrane of Halobacterium salinarum, functions as a light-driven proton pump. A 3-D crystal of bacteriorhodopsin, which was prepared by the membrane fusion method, was used to investigate structural changes in the primary photoreaction. It was observed that when a frozen crystal was exposed to a low flux of X-ray radiation (5 x 10(14)photons mm(-2)), nearly half of the protein was converted into an orange species, exhibiting absorption peaks at 450 nm, 478 nm and 510 nm. The remainder retained the normal photochemical activity until Asp85 in the active site was decarboxlyated by a higher flux of X-ray radiation (10(16)photons mm(-2)). The procedure of diffraction measurement was improved so as to minimize the effects of the radiation damage and determine the true structural change associated with the primary photoreaction. Our structural model of the K intermediate indicates that the Schiff base linkage and the adjacent bonds in the polyene chain of retinal are largely twisted so that the Schiff base nitrogen atom still interacts with a water molecule located near Asp85. With respect to the other part of the protein, no appreciable displacement is induced in the primary photoreaction.

PubMed: 12445782
DOI: 10.1016/S0022-2836(02)01110-5

Experimental method

X-RAY DIFFRACTION (2.6 Å)