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1dze

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1dze, resolution 2.50Å ()
Sites: , , , , , , , and
Ligands: , , , , , , ,
Related: 1c3w, 1brd, 2brd, 1brr, 1bac, 1bad, 1bha, 1bhb, 1bct, 1ap9, 1at9, 1qm8
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



STRUCTURE OF THE M INTERMEDIATE OF BACTERIORHODOPSIN TRAPPED AT 100K

Publication Abstract from PubMed

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

1dze is a 1 chain structure with sequence from Halobacterium salinarum. The March 2002 RCSB PDB Molecule of the Month feature on Bacteriorhodopsin by David S. Goodsell is 10.2210/rcsb_pdb/mom_2002_3. 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
  • Sato H, Takeda K, Tani K, Hino T, Okada T, Nakasako M, Kamiya N, Kouyama T. Specific lipid-protein interactions in a novel honeycomb lattice structure of bacteriorhodopsin. Acta Crystallogr D Biol Crystallogr. 1999 Jul;55(Pt 7):1251-6. PMID:10393291

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