PDBsum entry 1vgo

Proton transport

PDB id: 1vgo

Contents

Protein chains

233 a.a. *

Ligands

BNG ×12

SO4 ×3

RET ×2

Waters ×29

* Residue conservation analysis

PDB id:

1vgo

Name:

Proton transport

Title:

Crystal structure of archaerhodopsin-2

Structure:

Archaerhodopsin 2. Chain: a, b. Synonym: ar 2

Source:

Halobacterium sp.. Organism_taxid: 29285. Strain: aus-2

Resolution:

2.50Å R-factor: 0.241 R-free: 0.268

Authors:

K.Yoshimura,N.Enami,M.Murakami,H.Okumura,K.Ihara,T.Kouyama

Key ref:

N.Enami et al. (2006). Crystal structures of archaerhodopsin-1 and -2: Common structural motif in archaeal light-driven proton pumps. J Mol Biol, 358, 675-685. PubMed id: 16540121 DOI: 10.1016/j.jmb.2006.02.032

Date:

28-Apr-04 Release date: 04-Oct-05

Protein chains

P29563  (BACR2_HALS2) -  Archaerhodopsin-2 from Halobacterium sp. (strain aus-2)

Seq: 259 a.a.

Struc: 233 a.a.

DOI no: 10.1016/j.jmb.2006.02.032

J Mol Biol 358:675-685 (2006)

PubMed id: 16540121

Crystal structures of archaerhodopsin-1 and -2: Common structural motif in archaeal light-driven proton pumps.

N.Enami, K.Yoshimura, M.Murakami, H.Okumura, K.Ihara, T.Kouyama.

ABSTRACT

Archaerhodopsin-1 and -2 (aR-1 and aR-2) are light-driven proton pumps found in Halorubrum sp. aus-1 and -2, which share 55-58% sequence identity with bacteriorhodopsin (bR), a proton pump found in Halobacterium salinarum. In this study, aR-1 and aR-2 were crystallized into 3D crystals belonging to P4(3)2(1)2 (a = b = 128.1 A, c = 117.6 A) and C222(1) (a = 122.9 A, b = 139.5 A, c = 108.1 A), respectively. In both the crystals, the asymmetric unit contains two protein molecules with slightly different conformations. Each subunit is composed of seven helical segments as seen in bR but, unlike bR, aR-1 as well as aR-2 has a unique omega loop near the N terminus. It is found that the proton pathway in the extracellular half (i.e. the proton release channel) is more opened in aR-2 than in aR-1 or bR. This structural difference accounts for a large variation in the pKa of the acid purple-to-blue transition among the three proton pumps. All the aromatic residues surrounding the retinal polyene chain are conserved among the three proton pumps, confirming a previous argument that these residues are required for the stereo-specificity of the retinal isomerization. In the cytoplasmic half, the region surrounded by helices B, C and G is highly conserved, while the structural conservation is very low for residues extruded from helices E and F. Structural conservation of the hydrophobic residues located on the proton uptake pathway suggests that their precise arrangement is necessary to prevent a backward flow of proton in the presence of a large pH gradient and membrane potential. An empty cavity is commonly seen in the vicinity of Leu93 contacting the retinal C13 methyl. Existence of such a cavity is required to allow a large rotation of the side-chain of Leu93 at the early stage of the photocycle, which has been shown to accompany water translocation across the Schiff base.

Selected figure(s)

Figure 6.
Figure 6. Structural comparison of the cytoplasmic halves of aR-1, aR-2 and bR. Carbon atoms in aR-2 (subunit-I), aR-1(subunit-I) and bR are drawn in gold, yellow and cyan, respectively, and nitrogen and oxygen atoms in all the proteins are in blue and red, respectively.

Figure 7.
Figure 7. Micro-cavities in the light-adapted states of aR-2 (a), aR-1 (b) and bR (c) and in the L intermediate of bR (d). In (a) and (b), two subunits contained in the asymmetric unit are superimposed and micro-cavities in the subunits I and II are drawn in yellow and cyan, respectively; the micro-cavities observed commonly in both the subunits are in green. In (c) and (d), micro-cavities are drawn in cyan. Some important residues (Arg82, Leu93, Asp96, Lys216 and retinal) are represented with a ball-and-stick model. Red spheres in (a), (c) and (d) represent water molecules. Since the proton release channel in aR-2 is so opened that cavity VI is actually connected to the solvent region, this cavity is visualized by placing an artificial polypeptide near the outlet of the proton release channel. This Figure was drawn with Swiss-PdbViewer.^48

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 358, 675-685) copyright 2006.

Figures were selected by the author.

Author's comment

The structures of the trimeric archaerhodopsin-2-bacterioruberin complex in a trigonal P321 crystal and a hexagonal P6(3) crystal have recently been reported by Yoshimura and Kouyama (J. Mol. Biol., 375, 1267-1281, 2008). Their crystal coordinates are deposited in the PDB (accession code 2EI4 and 2Z55).