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

PDB id:

6prc

Name:

Photosynthetic reaction center

Title:

Photosynthetic reaction center from rhodopseudomonas viridis (dg- 420314 (triazine) complex)

Structure:

Photosynthetic reaction center. Chain: c. Photosynthetic reaction center. Chain: l. Photosynthetic reaction center. Chain: m. Photosynthetic reaction center. Chain: h

Source:

Blastochloris viridis. Organism_taxid: 1079. Atcc: dsm 133. Collection: dsm 133. Cellular_location: intracytoplasmic membrane (icm). Cellular_location: intracytoplasmic membrane (icm)

Biol. unit:

Tetramer (from PQS)

Resolution:

2.30Å R-factor: 0.184 R-free: 0.225

Authors:

C.R.D.Lancaster,H.Michel

Key ref:

C.R.Lancaster and H.Michel (1999). 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. J Mol Biol, 286, 883-898. PubMed id: 10024457 DOI: 10.1006/jmbi.1998.2532

Date:

31-Jul-97 Release date: 06-Apr-99

Protein chain

P07173  (CYCR_BLAVI) -  Photosynthetic reaction center cytochrome c subunit from Blastochloris viridis

Seq: 356 a.a.

Struc: 332 a.a.

Protein chain

P06009  (RCEL_BLAVI) -  Reaction center protein L chain from Blastochloris viridis

Seq: 274 a.a.

Struc: 273 a.a.

Protein chain

P06010  (RCEM_BLAVI) -  Reaction center protein M chain from Blastochloris viridis

Seq: 324 a.a.

Struc: 323 a.a.

Protein chain

P06008  (RCEH_BLAVI) -  Reaction center protein H chain from Blastochloris viridis

Seq: 258 a.a.

Struc: 258 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1006/jmbi.1998.2532

J Mol Biol 286:883-898 (1999)

PubMed id: 10024457

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.

C.R.Lancaster, H.Michel.

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.

Selected figure(s)

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.

Figures were selected by an automated process.