PDBsum entry 1r3p

Transport protein

PDB id: 1r3p

Contents

Protein chain

228 a.a.

Ligands

RET

Waters ×30

Superseded by:

1vjm

PDB id:

1r3p

Name:

Transport protein

Title:

Deformation of helix c in the low-temperature l- intermediate of bacteriorhyodopsin

Structure:

Bacteriorhodopsin. Chain: a. Synonym: br

Source:

Halobacterium sp.. Archaea. Strain: s9

Biol. unit:

Trimer (from PQS)

Resolution:

2.30Å R-factor: 0.252 R-free: 0.298

Authors:

K.Edman,A.Royant,G.Larsson,F.Jacobson,T.Taylor,D.Van Der Spoel,E.M.Landau,E.Pebay-Peyroula,R.Neutze

Key ref:

K.Edman et al. (2004). Deformation of helix C in the low temperature L-intermediate of bacteriorhodopsin. J Biol Chem, 279, 2147-2158. PubMed id: 14532280 DOI: 10.1074/jbc.M300709200

Date:

02-Oct-03 Release date: 27-Jan-04

Protein chain

P02945  (BACR_HALSA) -  Bacteriorhodopsin from Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)

Seq: 262 a.a.

Struc: 228 a.a.

DOI no: 10.1074/jbc.M300709200

J Biol Chem 279:2147-2158 (2004)

PubMed id: 14532280

Deformation of helix C in the low temperature L-intermediate of bacteriorhodopsin.

K.Edman, A.Royant, G.Larsson, F.Jacobson, T.Taylor, D.van der Spoel, E.M.Landau, E.Pebay-Peyroula, R.Neutze.

ABSTRACT

X-ray and electron diffraction studies of specific reaction intermediates, or reaction intermediate analogues, have produced a consistent picture of the structural mechanism of light-driven proton pumping by bacteriorhodopsin. Of central importance within this picture is the structure of the L-intermediate, which follows the retinal all-trans to 13-cis photoisomerization step of the K-intermediate and sets the stage for the primary proton transfer event from the positively charged Schiff base to the negatively charged Asp-85. Here we report the structural changes in bacteriorhodopsin following red light illumination at 150 K. Single crystal microspectrophotometry showed that only the L-intermediate is populated in three-dimensional crystals under these conditions. The experimental difference Fourier electron density map and refined crystallographic structure were consistent with those previously presented (Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2000) Nature 406, 645-648; Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2001) Photochem. Photobiol. 74, 794-804). Based on the refined crystallographic structures, molecular dynamic simulations were used to examine the influence of the conformational change of the protein that is associated with the K-to-L transition on retinal dynamics. Implications regarding the structural mechanism for proton pumping by bacteriorhodopsin are discussed.

Selected figure(s)

Figure 2.
FIG. 2. Long distance overview of the F[exc]-F[gnd] difference Fourier electron density maps resulting from green light illumination at 110 K contoured at 4.0 (a), red light illumination at 150 K contoured at 3.2 (b), and green light illumination at 170 K contoured at 3.4 (c). Positive electron density changes are colored blue, and negative electron density changes are colored yellow. More details of the trapping protocols are given in the text. Overviews of the difference density maps depicted in a and c can be found in stereo in Refs. 10 and 1, respectively.

Figure 6.
FIG. 6. Light-induced changes in the EC H-bond network. a, the location of water molecules in bR. b, the location of water molecules in L[LT]. Figs. 2, 3, 4, 5, 6 were drawn using the Swiss PDB Viewer (102).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 2147-2158) copyright 2004.

Figures were selected by an automated process.