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

References listed in PDB file

Key reference

Title

Determination of the binding sites of the proton transfer inhibitors cd2+ and zn2+ in bacterial reaction centers.

Authors

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

Ref.

Proc Natl Acad Sci U S A, 2000, 97, 1542-1547. [DOI no: 10.1073/pnas.97.4.1542]

PubMed id

10677497

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.

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.

Secondary reference #1

Title

Identification of the proton pathway in bacterial reaction centers: inhibition of proton transfer by binding of zn2+ or cd2+.

Authors

M.L.Paddock, M.S.Graige, G.Feher, M.Y.Okamura.

Ref.

Proc Natl Acad Sci U S A, 1999, 96, 6183-6188. [DOI no: 10.1073/pnas.96.11.6183]

PubMed id

10339562

Figure 1.
Fig. 1. Absorbance decay of the semiquinones at 450 nm as a function of time after the second of two laser flashes in the presence of various concentrations of ZnSO[4] (a) and CdSO[4] (b). From the decay, the rate constant k[AB]^(2) was determined. Note the slowing of the kinetics with increasing cation concentrations. The pedestal at long times after the laser flash is caused by the absorbance change of the cytochrome c used to reduce the primary donor (see Materials and Methods). Conditions were: 2 µM RCs in 10 mM Tris·HCl (pH 7.7), 0.25% lauryl dimethylamine-N-oxide with the concentration of ZnSO[4] or CdSO[4] as indicated in the figure.

Figure 4.
Fig. 4. Part of the RC structure near the secondary quinone, Q[B] binding site, as determined for the Q[B]^ state by Stowell et al. (18). Possible proton transfer pathways (P1-P3) proposed by Abresch et al. (19) are shown by dashed lines. One carbonyl oxygen of Q[B] is located near Ser-L223 and the backbone NH of Ile-L224 (not shown); the other carbonyl oxygen of Q[B] is located near His-L190. Nearby are two carboxylic acid groups Asp-L213 and Glu-L212 that have been implicated in proton transfer to reduced Q[B] (reactions 2a and 2b, respectively) (8-13) and to which the proton transfer pathways lead. Also shown are a His cluster (consisting of H68, H126, and H128) and a carboxylic acid cluster (consisting of Asp-L213, Asp-L210, Asp-M17, Glu-H173, Asp-H170, and Asp-M124).

Secondary reference #2

Title

Identification of proton transfer pathways in the X-Ray crystal structure of the bacterial reaction center from rhodobacter sphaeroides

Authors

E.C.Abresch, M.L.Paddock, M.H.B.Stowell, T.M.Mcphillips, H.L.Axelrod, S.M.Soltis, D.C.Rees, M.Y.Okamura, G.Feher.

Ref.

photosynth res, 1998, 55, 119.

Secondary reference #3

Title

Light-Induced structural changes in photosynthetic reaction center: implications for mechanism of electron-Proton transfer.

Authors

M.H.Stowell, T.M.Mcphillips, D.C.Rees, S.M.Soltis, E.Abresch, G.Feher.

Ref.

Science, 1997, 276, 812-816. [DOI no: 10.1126/science.276.5313.812]

PubMed id

9115209

Figure 4.
Fig. 4. Superposition of previously reported positions of ubiquinone in the Q[B] binding pocket [see also (4)]. PDB (Protein Data^ Bank, Brookhaven) entries and color code: 1PCR, Ermler et al. (8), yellow; 2RCR, Chang et al. (6), dark blue; 1YST, Arnoux et al. (7), green; 4RCR, Allen et al. (5), red; present model of the dark structure, light blue. Superposition was performed^ by the method of Kabsch (52). Side chain residues from the current dark structure are indicated. Oxygen, nitrogen, and carbon atoms are colored red, blue, and gray, respectively.

Figure 5.
Fig. 5. Water channels P1 and P2 observed in the dark RC structure leading from the Q[B] pocket to the surface of the protein on the^ cytoplasmic side of the RC. The coloring scheme is: H subunit (green), L subunit (yellow), M subunit (blue), water molecules (red), bacteriochlorophylls (green), and bacteriopheophytin (purple). Q[A] and Q[B] are colored orange-red, while the nonheme iron is rust-colored. The positions of the quinone tails past carbon C16 are less well defined because of poor electron density. The approximate location of the membrane is indicated by the shaded region. The details of the P1 and P2 pathways are shown in Fig. 6, A and B.

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