PDBsum entry 1p8h

Proton transport

PDB id: 1p8h

Contents

Protein chain

222 a.a. *

Ligands

RET

LI1 ×13

SQU

Waters ×25

* Residue conservation analysis

PDB id:

1p8h

Name:

Proton transport

Title:

Bacteriorhodopsin m1 intermediate produced at room temperature

Structure:

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

Source:

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

Biol. unit:

Trimer (from PDB file)

Resolution:

1.52Å R-factor: 0.172 R-free: 0.207

Ensemble:

2 models

Authors:

J.K.Lanyi

Key ref:

B.Schobert et al. (2003). Crystallographic structures of the M and N intermediates of bacteriorhodopsin: assembly of a hydrogen-bonded chain of water molecules between Asp-96 and the retinal Schiff base. J Mol Biol, 330, 553-570. PubMed id: 12842471 DOI: 10.1016/S0022-2836(03)00576-X

Date:

07-May-03 Release date: 07-Jul-03

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(03)00576-X

J Mol Biol 330:553-570 (2003)

PubMed id: 12842471

Crystallographic structures of the M and N intermediates of bacteriorhodopsin: assembly of a hydrogen-bonded chain of water molecules between Asp-96 and the retinal Schiff base.

B.Schobert, L.S.Brown, J.K.Lanyi.

ABSTRACT

An M intermediate of wild-type bacteriorhodopsin and an N intermediate of the V49A mutant were accumulated in photostationary states at pH 5.6 and 295 K, and their crystal structures determined to 1.52A and 1.62A resolution, respectively. They appear to be M(1) and N' in the sequence, M(1)<-->M(2)<-->M'(2)<-->N<-->N'-->O-->BR, where M(1), M(2), and M'(2) contain an unprotonated retinal Schiff base before and after a reorientation switch and after proton release to the extracellular surface, while N and N' contain a reprotonated Schiff base, before and after reprotonation of Asp96 from the cytoplasmic surface. In M(1), we detect a cluster of three hydrogen-bonded water molecules at Asp96, not present in the BR state. In M(2), whose structure we reported earlier, one of these water molecules intercalates between Asp96 and Thr46. In N', the cluster is transformed into a single-file hydrogen-bonded chain of four water molecules that connects Asp96 to the Schiff base. We find a network of three water molecules near residue 219 in the crystal structure of the non-illuminated F219L mutant, where the residue replacement creates a cavity. This suggests that the hydration of the cytoplasmic region we observe in N' might have occurred spontaneously, beginning at an existing water molecule as nucleus, in the cavities from residue rearrangements in the photocycle.

Selected figure(s)

Figure 3.
Figure 3. Absorption changes after flash photo-excitation of (a) membrane fragments of wild-type bacteriorhodopsin, (b) membrane fragments of the V49A mutant, and (c) crystals of the V49A mutant. Conditions: (a) 1 M NaCl, 50 mM Mes (pH 5.9), 25 °C; (b) 1 M NaCl, 50 mM Mes (pH 6.1), 25 °C; (c) 3 M potassium sodium phosphate (pH 5.6), 23 °C.

Figure 4.
Figure 4. The 2F[obs] -F[calc] map of the hydrogen-bonding pattern in the region between the retinal Schiff base and Asp96 in illuminated V49A bacteriorhodopsin (containing the BR and N' states). Colors: green, BR state; and atomic colors, intermediate N'. The contour levels are at 1s. Hydrogen bonds are shown in gold, with their lengths in Å.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 330, 553-570) copyright 2003.

Figures were selected by an automated process.