6PRC

PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (DG-420314 (TRIAZINE) COMPLEX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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.

Lancaster, C.R.Michel, H.

(1999) J.Mol.Biol. 286: 883-898

  • DOI: 10.1006/jmbi.1998.2532
  • Primary Citation of Related Structures:  
  • Also Cited By: 2JBL, 1DXR

  • PubMed 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). ...

    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.


    Related Citations: 
    • Ubiquinone Reduction and Protonation in the Reaction Centre of Rhodopseudomonas Viridis: X-Ray Structures and Their Functional Implications
      Lancaster, C.R.D.
      (1998) Biochim.Biophys.Acta 1365: 143
    • Structure of the Protein Subunits in the Photosynthetic Reaction Centre of Rhodopseudomonas Viridis at 3 Angstroms Resolution
      Deisenhofer, J.,Epp, O.,Miki, K.,Huber, R.,Michel, H.
      (1985) Nature 318: 618
    • 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
      Deisenhofer, J.,Epp, O.,Miki, K.,Huber, R.,Michel, H.
      (1984) J.Mol.Biol. 180: 385
    • The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas Viridis
      Deisenhofer, J.,Michel, H.
      (1989) Science 245: 1463
    • Three-Dimensional Crystals of a Membrane Protein Complex. The Photosynthetic Reaction Centre from Rhodopseudomonas Viridis
      Michel, H.
      (1982) J.Mol.Biol. 158: 567
    • 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
      Lancaster, C.R.,Michel, H.
      (1997) Structure 5: 1339
    • Crystallographic Refinement at 2.3 A Resolution and Refined Model of the Photosynthetic Reaction Centre from Rhodopseudomonas Viridis
      Deisenhofer, J.,Epp, O.,Sinning, I.,Michel, H.
      (1995) J.Mol.Biol. 246: 429


    Organizational Affiliation

    Abteilung Molekulare Membranbiologie, Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Str. 7, Frankfurt am Main, D-60528, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
C
336Blastochloris viridisMutation(s): 0 
Gene Names: pufC (cytC)
Find proteins for P07173 (Blastochloris viridis)
Go to UniProtKB:  P07173
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
L
273Blastochloris viridisMutation(s): 0 
Gene Names: pufL
Find proteins for P06009 (Blastochloris viridis)
Go to UniProtKB:  P06009
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
M
323Blastochloris viridisMutation(s): 0 
Gene Names: pufM
Find proteins for P06010 (Blastochloris viridis)
Go to UniProtKB:  P06010
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
H
258Blastochloris viridisMutation(s): 0 
Gene Names: puhA
Find proteins for P06008 (Blastochloris viridis)
Go to UniProtKB:  P06008
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
H, M
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
LDA
Query on LDA

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Download CCD File 
H, L, M
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
CEB
Query on CEB

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Download CCD File 
L
2-CHLORO-4-ETHYLAMINO-6-(S(-)-2'-CYANO-4-BUTYLAMINO)-1,3,5-TRIAZINE
DG-420314
C10 H15 Cl N6
IUCVBFHDSFSEIK-JTQLQIEISA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
MQ7
Query on MQ7

Download SDF File 
Download CCD File 
M
MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
 Ligand Interaction
FE2
Query on FE2

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Download CCD File 
M
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
BPB
Query on BPB

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L, M
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
 Ligand Interaction
BCB
Query on BCB

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Download CCD File 
L, M
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-LQPBATPMDK
 Ligand Interaction
NS5
Query on NS5

Download SDF File 
Download CCD File 
M
15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
H
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 223.500α = 90.00
b = 223.500β = 90.00
c = 113.600γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
X-PLORphasing
X-PLORrefinement
AGROVATA)data scaling
X-PLORmodel building
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-04-06
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model