PDBsum entry 1m0m

Ion transport

PDB id: 1m0m

Contents

Protein chain

222 a.a. *

Ligands

RET

LI1 ×13

SQU

Waters ×23

* Residue conservation analysis

PDB id:

1m0m

Name:

Ion transport

Title:

Bacteriorhodopsin m1 intermediate at 1.43 a resolution

Structure:

Bacteriorhodopsin. Chain: a. Synonym: br. Engineered: yes

Source:

Halobacterium salinarum. Organism_taxid: 2242. Cellular_location: plasma membrane. Expressed in: halobacterium salinarum. Expression_system_taxid: 2242.

Resolution:

1.43Å R-factor: 0.164 R-free: 0.213

Ensemble:

2 models

Authors:

J.K.Lanyi

Key ref:

J.Lanyi and B.Schobert (2002). Crystallographic structure of the retinal and the protein after deprotonation of the Schiff base: the switch in the bacteriorhodopsin photocycle. J Mol Biol, 321, 727-737. PubMed id: 12206786 DOI: 10.1016/S0022-2836(02)00682-4

Date:

13-Jun-02 Release date: 11-Sep-02

Protein chain

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

Seq: 262 a.a.

Struc: 222 a.a.

DOI no: 10.1016/S0022-2836(02)00682-4

J Mol Biol 321:727-737 (2002)

PubMed id: 12206786

Crystallographic structure of the retinal and the protein after deprotonation of the Schiff base: the switch in the bacteriorhodopsin photocycle.

J.Lanyi, B.Schobert.

ABSTRACT

We illuminated bacteriorhodopsin crystals at 210K to produce, in a photostationary state with 60% occupancy, the earliest M intermediate (M1) of the photocycle. The crystal structure of this state was then determined from X-ray diffraction to 1.43 A resolution. When the refined model is placed after the recently determined structure for the K intermediate but before the reported structures for two later M states, a sequence of structural changes becomes evident in which movements of protein atoms and bound water are coordinated with relaxation of the initially strained photoisomerized 13-cis,15-anti retinal. In the K state only retinal atoms are displaced, but in M1 water 402 moves also, nearly 1A away from the unprotonated retinal Schiff base nitrogen. This breaks the hydrogen bond that bridges them, and initiates rearrangements of the hydrogen-bonded network of the extracellular region that develop more fully in the intermediates that follow. In the M1 to M2 transition, relaxation of the C14-C15 and C15=NZ torsion angles to near 180 degrees reorients the retinylidene nitrogen atom from the extracellular to the cytoplasmic direction, water 402 becomes undetectable, and the side-chain of Arg82 is displaced strongly toward Glu194 and Glu204. Finally, in the M2 to M2' transition, correlated with release of a proton to the extracellular surface, the retinal assumes a virtually fully relaxed bent shape, and the 13-methyl group thrusts against the indole ring of Trp182 which tilts in the cytoplasmic direction. Comparison of the structures of M1 and M2 reveals the principal switch in the photocycle: the change of the angle of the C15=NZ-CE plane breaks the connection of the unprotonated Schiff base to the extracellular side and establishes its connection to the cytoplasmic side.

Selected figure(s)

Figure 2.
Figure 2. The 2F[obs] -F[calc] electron density maps at the retinal Schiff base for (a) an illuminated crystal and (b) a non-illuminated crystal. In both cases, refinement assumed two conformations, at occupancies of 40% (unconverted BR state, green) and 60% (M[1] state, grey), respectively, as discussed in the text. Some atom notations in the retinal are given in (b). The Figure was prepared with graphics program Setor.[60]

Figure 3.
Figure 3. The 2F[obs] -F[calc] electron density maps at the retinal, Asp85, Asp212 and water 402 for (a) an illuminated crystal and (b) a non-illuminated crystal. As in Figure 2, the two conformations, for the BR and M[1] states are indicated with green and gray colors. The retinal Schiff base is labeled as NZ. In (a) the hydrogen-bonds (in blue) are for the M[1] state, in (b) they are (in yellow) for the BR state. The Figure was prepared with the graphics program Setor.[60]

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 321, 727-737) copyright 2002.

Figures were selected by an automated process.