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1iw9
From Proteopedia
| 1iw9, resolution 2.50Å () | |||||||||
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| Sites: | , , , , , , , and | ||||||||
| Ligands: | , , , , , | ||||||||
| Related: | 1dze, 1iw6 | ||||||||
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| Resources: | FirstGlance, OCA, PDBsum, RCSB, TOPSAN | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Crystal Structure of the M Intermediate of Bacteriorhodopsin
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.
Crystal structure of the M intermediate of bacteriorhodopsin: allosteric structural changes mediated by sliding movement of a transmembrane helix., Takeda K, Matsui Y, Kamiya N, Adachi S, Okumura H, Kouyama T, J Mol Biol. 2004 Aug 20;341(4):1023-37. PMID:15328615
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
About this Structure
1iw9 is a 1 chain structure with sequence from Halobacterium salinarum. Full crystallographic information is available from OCA.
Reference
- 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. 2004 Aug 20;341(4):1023-37. PMID:15328615
- 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. 2004 Jan 9;335(2):531-46. PMID:14672661
