PDBsum entry 3a0b

Electron transport

PDB id: 3a0b

Contents

Protein chains

335 a.a.

485 a.a.

447 a.a.

340 a.a.

82 a.a.

35 a.a.

64 a.a.

35 a.a.

34 a.a.

36 a.a.

37 a.a.

36 a.a.

242 a.a.

30 a.a.

98 a.a.

137 a.a.

34 a.a.

28 a.a.

24 a.a.

62 a.a.

Ligands

OEC ×2

CLA ×70

PHO ×4

PQ9 ×4

BCR ×22

LHG ×2

MGE ×8

DGD ×8

HEM ×4

Metals

_BR ×4

FE2 ×2

References listed in PDB file

Key reference

Title

Location of chloride and its possible functions in oxygen-Evolving photosystem ii revealed by x-Ray crystallography.

Authors

K.Kawakami, Y.Umena, N.Kamiya, J.R.Shen.

Ref.

Proc Natl Acad Sci U S A, 2009, 106, 8567-8572. [DOI no: 10.1073/pnas.0812797106]

PubMed id

19433803

Abstract

The chloride ion, Cl(-), is an essential cofactor for oxygen evolution of photosystem II (PSII) and is closely associated with the Mn(4)Ca cluster. Its detailed location and function have not been identified, however. We substituted Cl(-) with a bromide ion (Br(-)) or an iodide ion (I(-)) in PSII and analyzed the crystal structures of PSII with Br(-) and I(-) substitutions. Substitution of Cl(-) with Br(-) did not inhibit oxygen evolution, whereas substitution of Cl(-) with I(-) completely inhibited oxygen evolution, indicating the efficient replacement of Cl(-) by I(-). PSII with Br(-) and I(-)substitutions were crystallized, and their structures were analyzed. The results showed that there are 2 anion-binding sites in each PSII monomer; they are located on 2 sides of the Mn(4)Ca cluster at equal distances from the metal cluster. Anion-binding site 1 is close to the main chain of D1-Glu-333, and site 2 is close to the main chain of CP43-Glu-354; these 2 residues are coordinated directly with the Mn(4)Ca cluster. In addition, site 1 is located in the entrance of a proton exit channel. These results indicate that these 2 Cl(-) anions are required to maintain the coordination structure of the Mn(4)Ca cluster as well as the proposed proton channel, thereby keeping the oxygen-evolving complex fully active.

Figure 3.
Location of the 2 anion-binding sites in PSII. (A) Composite omit Fo-Fc map (blue) and anomalous map (red) of PSII with Br^− substitution contoured at σ = 1.0 and 4.0, respectively, superimposed on the structure of the Mn[4]Ca cluster and its surrounding regions. The structure of PSII with Br^−substitution was shown by the molecular replacement method with the structure of the PDB code 2AXT as the search model. Color codes for the residues are as follows: yellow, D1; green, D2; orange, CP43; purple, Mn atoms. (B) Composite omit Fo-Fc map (blue) and anomalous map (red) of I^−-substituted PSII contoured at σ = 1.0 and 4.0, respectively, superimposed on the structure of the Mn[4]Ca cluster and its surrounding regions. The structure of PSII with I^− substitution was shown by the molecular replacement method. The color codes for the residues are the same as in A. (C) Location of Br[1] relative to the proton exit channel proposed in (16, 27–29). The residues of PsbO are drawn in blue, and the residues of other subunits are in the same colors as in A. The directions of atoms from Cα to Cβ in the residues are indicated by capsule-shaped objects.

Figure 4.
Additional binding sites of I^− in I^−-substituted PSII. (A) Fo-Fc omit map of PSII with I^− substitution (red) contoured at σ = 3.0, superimposed on the structure of CP47 (green) obtained by the molecular replacement method, showing the association of I^− with CP47-Cys-112. (B) Fo-Fc omit map of PSII with I^− substitution (red) contoured at σ = 3.0, superimposed on the structure of PsbTc (pink), showing the association of I^− with PsbTc-Cys-12. The capsule-shaped objects show the direction of atoms from Cα to Cβ in the 2 Cys residues. (C) 2Fo-Fc map (blue, σ = 1.0) and omit Fo-Fc map (red, σ = 2.0) of PSII with I^− substitution around the region of D2-Tyr-160(Y[D]), together with the structure of D2 (green) in this region.