PDBsum entry 1ds8

Photosynthesis

PDB id: 1ds8

Contents

Protein chains

281 a.a. *

299 a.a. *

246 a.a. *

Ligands

BCL ×8

BPH ×4

U10 ×4

LDA ×6

Metals

_CD ×2

FE2 ×2

_CL ×2

Waters ×582

* Residue conservation analysis

PDB id:

1ds8

Name:

Photosynthesis

Title:

Photosynthetic reaction center from rhodobacter sphaeroides in the charge-neutral dqaqb state with the proton transfer inhibitor cd2+

Structure:

Reaction center protein l chain. Chain: l, r. Reaction center protein m chain. Chain: m, s. Reaction center protein h chain. Chain: h, t

Source:

Rhodobacter sphaeroides. Organism_taxid: 1063. Organism_taxid: 1063

Biol. unit:

Trimer (from PQS)

Resolution:

2.50Å R-factor: 0.227 R-free: 0.256

Authors:

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

Key ref:

H.L.Axelrod et al. (2000). Determination of the binding sites of the proton transfer inhibitors Cd2+ and Zn2+ in bacterial reaction centers. Proc Natl Acad Sci U S A, 97, 1542-1547. PubMed id: 10677497 DOI: 10.1073/pnas.97.4.1542

Date:

07-Jan-00 Release date: 08-Mar-00

Protein chains

P0C0Y8  (RCEL_CERSP) -  Reaction center protein L chain from Cereibacter sphaeroides

Seq: 282 a.a.

Struc: 281 a.a.

Protein chains

P0C0Y9  (RCEM_CERSP) -  Reaction center protein M chain from Cereibacter sphaeroides

Seq: 308 a.a.

Struc: 299 a.a.

Protein chains

P0C0Y7  (RCEH_CERSP) -  Reaction center protein H chain from Cereibacter sphaeroides

Seq: 260 a.a.

Struc: 246 a.a.

Enzyme reactions

• Enzyme class: Chains L, M, H, R, S, T: E.C.?

DOI no: 10.1073/pnas.97.4.1542

Proc Natl Acad Sci U S A 97:1542-1547 (2000)

PubMed id: 10677497

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

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

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 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.

Selected figure(s)

Figure 2.
Fig. 2. Stereoview of the Cd^2+ binding site (orange) on the RC from Rb. sphaeroides. The six Cd^2+ ligands are His-H126, His-H128, Asp-H124 (green), and three water molecules (red). Two nearby aspartic acid residues, Asp-L210 (yellow) and Asp-M17 (blue), are part of a hydrogen bonding network that leads from the metal site to Q[B] (see Fig. 5). |F[o]| |F[c]| difference electron density (purple) is contoured at 2.5 and superimposed on the structure. To reduce phase bias, ligands were excluded in the calculation of the map.

Figure 5.
Fig. 5. Stereo representation of hydrogen bonding networks in the charge-separated (D^+Q[A]Q[B] ) state of the native RC (7, 18) from Rb. sphaeroides spanning the region between the Cd^2+ (or Zn2+) binding site (indicated by arrow) and Q[B] . L subunit (yellow), M subunit (blue), and H subunit (green), and Q[B] and water molecules (red). Dashed lines represent hydrogen bonds. Wat-72 is displaced when Cd^2+ or Zn2+ binds. The metal ion is located at the proton entry point.

Figures were selected by an automated process.