1DV6

PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-NEUTRAL DQAQB STATE WITH THE PROTON TRANSFER INHIBITOR ZN2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Determination of the binding sites of the proton transfer inhibitors Cd2+ and Zn2+ in bacterial reaction centers.

Axelrod, H.L.Abresch, E.C.Paddock, M.L.Okamura, M.Y.Feher, G.

(2000) Proc.Natl.Acad.Sci.USA 97: 1542-1547

  • Primary Citation of Related Structures:  1DS8, 1DV3

  • PubMed Abstract: 
  • The reaction center (RC) from Rhodobacter sphaeroides couples light-driven electron transfer to protonation of a bound quinone acceptor molecule, Q(B), within the RC. The binding of Cd(2+) or Zn(2+) has been previously shown to inhibit the rate of re ...

    The reaction center (RC) from Rhodobacter sphaeroides couples light-driven electron transfer to protonation of a bound quinone acceptor molecule, Q(B), within the RC. The binding of Cd(2+) or Zn(2+) has been previously shown to inhibit the rate of reduction and protonation of Q(B). We report here on the metal binding site, determined by x-ray diffraction at 2.5-A resolution, obtained from RC crystals that were soaked in the presence of the metal. The structures were refined to R factors of 23% and 24% for the Cd(2+) and Zn(2+) complexes, respectively. Both metals bind to the same location, coordinating to Asp-H124, His-H126, and His-H128. The rate of electron transfer from Q(A)(-) to Q(B) was measured in the Cd(2+)-soaked crystal and found to be the same as in solution in the presence of Cd(2+). In addition to the changes in the kinetics, a structural effect of Cd(2+) on Glu-H173 was observed. This residue was well resolved in the x-ray structure-i.e., ordered-with Cd(2+) bound to the RC, in contrast to its disordered state in the absence of Cd(2+), which suggests that the mobility of Glu-H173 plays an important role in the rate of reduction of Q(B). The position of the Cd(2+) and Zn(2+) localizes the proton entry into the RC near Asp-H124, His-H126, and His-H128. Based on the location of the metal, likely pathways of proton transfer from the aqueous surface to Q(B) are proposed.


    Related Citations: 
    • Identification of proton transfer pathways in the X-ray crystal structure of the bacterial reaction center from Rhodobacter sphaeroides
      Abresch, E.C.,Paddock, M.L.,Stowell, M.H.B.,McPhillips, T.M.,Axelrod, H.L.,Soltis, S.M.,Rees, D.C.,Okamura, M.Y.,Feher, G.
      (1998) Photosynth.Res. 55: 119
    • A New Metal-Binding Site in Photosynthetic Bacterial Reaction Centers That Modulates QA to QB Electron Transfer
      Utschig, L.M.,Ohigashi, Y.,Thurnauer, M.C.,Tiede, D.M.
      (1998) Biochemistry 37: 8278
    • Light-Induced Structural Changes in Photosynthetic Reaction Center: Implications for Mechanism of Electron-Proton Transfer Electron- Proton Transfer
      Stowell, M.H.,McPhillips, T.M.,Rees, D.C.,Soltis, S.M.,Abresch, E.,Feher, G.
      (1997) Science 276: 812
    • Identification of the Proton Pathway in Bacterial Reaction Centers: Inhibition of Proton Transfer by Binding of Zn2+ or Cd2+
      Paddock, M.L.,Graige, M.S.,Feher, G.,Okamura, M.Y.
      (1999) Proc.Natl.Acad.Sci.USA 96: 6183


    Organizational Affiliation

    Department of Physics 0319, 9500 Gilman Drive, University of California at San Diego, La Jolla, CA 92093, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
L, R
281Rhodobacter sphaeroidesGene Names: pufL
Find proteins for P0C0Y8 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
M, S
307Rhodobacter sphaeroidesGene Names: pufM
Find proteins for P0C0Y9 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
H, T
260Rhodobacter sphaeroidesGene Names: puhA
Find proteins for P0C0Y7 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y7
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U10
Query on U10

Download SDF File 
Download CCD File 
L, M, R, S
UBIQUINONE-10
Coenzyme Q10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
H, T
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
M, S
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BCL
Query on BCL

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Download CCD File 
L, M, R, S
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
LDA
Query on LDA

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Download CCD File 
M, S
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

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M, S
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
BPH
Query on BPH

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L, M, R, S
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.238 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 141.517α = 90.00
b = 141.517β = 90.00
c = 278.506γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
CNSphasing
MOSFLMdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance