PDBsum entry 6prc

Photosynthetic reaction center

PDB id: 6prc

Contents

Protein chains

332 a.a. *

273 a.a. *

323 a.a. *

258 a.a. *

Ligands

HEM ×4

BCB ×4

BPB ×2

CEB

LDA ×6

SO4 ×4

MQ7

NS5

Metals

FE2

Waters ×337

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Refined crystal structures of reaction centres from rhodopseudomonas viridis in complexes with the herbicide atrazine and two chiral atrazine derivatives also lead to a new model of the bound carotenoid.

Authors

C.R.Lancaster, H.Michel.

Ref.

J Mol Biol, 1999, 286, 883-898. [DOI no: 10.1006/jmbi.1998.2532]

PubMed id

10024457

Abstract

In a reaction of central importance to the energetics of photosynthetic bacteria, light-induced electron transfer in the reaction centre (RC) is coupled with the uptake of protons from the cytoplasm at the binding site of the secondary quinone (QB). It has been established by X-ray crystallography that the triazine herbicide terbutryn binds to the QB site. However, the exact description of protein-triazine interactions has had to await the refinement of higher-resolution structures. In addition, there is also interest in the role of chirality in the activity of herbicides. Here, we report the structural characterisation of triazine binding by crystallographic refinement of complexes of the RC either with the triazine inhibitor atrazine (Protein Data Bank (PDB) entry 5PRC) or with the chiral atrazine derivatives, DG-420314 (S(-) enantiomer, PDB entry 6PRC) or DG-420315 (R(+) enantiomer, PDB entry 7PRC). Due to the high quality of the data collected, it has been possible to describe the exact nature of triazine binding and its effect on the structure of the protein at high-resolution limits of 2.35 A (5PRC), 2.30 A (6PRC), and 2.65 A (7PRC), respectively. In addition to two previously implied hydrogen bonds, a third hydrogen bond, binding the distal side of the inhibitors to the protein, and four additional hydrogen bonds mediated by two tightly bound water molecules on the proximal side of the inhibitors, are apparent. Based on the high quality data collected on the RC complexes of the two chiral atrazine derivatives, unequivocal assignment of the structure at the chiral centres was possible, even though the differences in structures of the substituents are small. The structures provide explanations for the relative binding affinities of the two chiral compounds. Although it was not an explicit goal of this work, the new data were of sufficient quality to improve the original model also regarding the structure of the bound carotenoid 1,2-dihydroneurosporene. A carotenoid model with a cis double bond at the 15,15' position fits the electron density better than the original model with a 13,14-cis double bond.

Figure 4.
Figure 4. Comparison of triazine and quinone binding to the Q[B] site (stereo views). Figures of three-dimensional molecular structures without electron density were generated with MolScript [Kraulis 1991]. (a) Stereo view; colour coding is as follows: RC complex with ubiquinone-2 (2PRC, black), with DG-420315 (7PRC, brown), with DG-420314 (6PRC, green), and with atrazine (5PRC, blue). (b) Side view of (a)).

Figure 5.
Figure 5. Hydrogen bonding interactions important for atrazine binding to the RC. (a) Carbon atoms are shown in black, nitrogen atoms in blue, oxygen in red, chlorine in green, and hydrogen atoms in white. (b) Comparison to the distal (green, 1PRC[new]) and proximal (black, 2PRC) ubiquinone binding sites [Lancaster and Michel 1997]. The structure of the atrazine complex (5PRC) is shown in pink.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 286, 883-898) copyright 1999.

Secondary reference #1

Title

Ubiquinone reduction and protonation in the reaction centre of rhodopseudomonas viridis: X-Ray structures and their functional implications

Author

C.R.D.Lancaster.

Ref.

biochim biophys acta, 1998, 1365, 143.

Secondary reference #2

Title

The coupling of light-Induced electron transfer and proton uptake as derived from crystal structures of reaction centres from rhodopseudomonas viridis modified at the binding site of the secondary quinone, Qb.

Authors

C.R.Lancaster, H.Michel.

Ref.

Structure, 1997, 5, 1339-1359. [DOI no: 10.1016/S0969-2126(97)00285-2]

PubMed id

9351808

Figure 3.
Figure 3. Comparison of the structure at the Q[B] site. (a-c) The RC-UQ2 complex (in black) compared to the original structure 1PRC [13] (in green). (d) The Q[B]-depleted RC (in pink) compared to the RC-UQ2 complex (in black). (e,f) The RC-stigmatellin complex (in orange) compared to that of the RC-UQ2 complex (in black). Prospective hydrogen bonds are represented as dashed lines. (Figure made with the program MOLSCRIPT [96].)

The above figure is reproduced from the cited reference with permission from Cell Press

Secondary reference #3

Title

Crystallographic refinement at 2.3 a resolution and refined model of the photosynthetic reaction centre from rhodopseudomonas viridis.

Authors

J.Deisenhofer, O.Epp, I.Sinning, H.Michel.

Ref.

J Mol Biol, 1995, 246, 429-457.

PubMed id

7877166

Secondary reference #4

Title

The photosynthetic reaction center from the purple bacterium rhodopseudomonas viridis.

Authors

J.Deisenhofer, H.Michel.

Ref.

Science, 1989, 245, 1463-1473.

PubMed id

17776797

Secondary reference #5

Title

Structure of the protein subunits in the photosynthetic reaction centre of rhodopseudomonas viridis at 3 angstroms resolution

Authors

J.Deisenhofer, O.Epp, K.Miki, R.Huber, H.Michel.

Ref.

nature, 1985, 318, 618.

Secondary reference #6

Title

X-Ray structure analysis of a membrane protein complex. Electron density map at 3 a resolution and a model of the chromophores of the photosynthetic reaction center from rhodopseudomonas viridis.

Authors

J.Deisenhofer, O.Epp, K.Miki, R.Huber, H.Michel.

Ref.

J Mol Biol, 1984, 180, 385-398. [DOI no: 10.1016/S0022-2836(84)80011-X]

PubMed id

6392571

Figure 3.
Fro. 3. Stereo draing of the special pair. The central local symmetry ais runs between the BChl-bs. Ring numbers are indicated in one BChl-b. Phytyl chains are truncated.

Figure 4.
FIG. 4. Stereo drawing of the prosthetic grups of the RC shwing 4 BChl-b (BC), 2 BPh-b (BP), 1 non-eine iron (Fe), 1 quinone (MQ) an heine grups (HE). The central local symmetry axis runs vertically in the plane of the picture. The plane of the membane is assumed t be oriented perpendicular to the central local symmetry axis, i.e. horizontal and perpendicular to the plane of th picture. The dotted lines marked 0 and I indicate the presmed approximate outer and inner membrane surfaces of the bacterial cell. The BChl-b, BPh-b, quinone and iron are lcated within th cylindrical central part of the RC compex; te ~ 70 A diameter of the cylinder is perpendicular to th local symmetry axis in the plane of the picture

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #7

Title

Three-Dimensional crystals of a membrane protein complex. The photosynthetic reaction centre from rhodopseudomonas viridis.

Author

H.Michel.

Ref.

J Mol Biol, 1982, 158, 567-572. [DOI no: 10.1016/0022-2836(82)90216-9]

PubMed id

7131557

Figure 1.
IG:. 1. Elation profile of the molecular siev chromatograph step used for the isolation of thr photosvnthetic reaction centrrs from tl. Gridis. I'hotosynthrtir membranes (I6 mg of protein/ml) were solubil&d in 5''' f. w/v) S.K~dod~c?ildimet,h~lamine A-oxide. WI O,> (y/v) Sx3. 10 mwTris_ HCI (pH 7) at room temprratre for 5 mill. After a clarifying spin (1OO,OOOg, 30 min). 09.5 ml of the supwnatant was applird to a. TSK 3ooO SW column (LKH. (ZrLfelfing) and run nt 0.1 ml/in in 20 mM-sodium phosphat,r (pH 7). 0.1 `)o (w/r) S,S-dodervldimc,th?aminr A-oxide, PI'',, (W/V) NaN,. The reaction crntres form the prak arktad I%(`.

The above figure is reproduced from the cited reference with permission from Elsevier