The structure of the Mn4Ca2+ cluster of photosystem II and its protein environment as revealed by X-ray crystallography

Abstract

The location, structure and protein environment of the Mn4Ca2+ cluster, which catalyses the light-driven, water-splitting reaction of photosystem II, has been revealed by X-ray crystallography. However, owing to the low resolutions of the crystal structures reported to date, and the possibility of radiation damage at the catalytic centre, the precise position of each metal ion remains unknown. To some extent, these problems have been overcome by applying spectroscopic techniques like extended X-ray absorption fine structure. Taking into account the most recent results obtained with these two X-ray-based techniques, we have attempted to refine models of the structure of the Mn4Ca2+ cluster and its protein environment.

Figure 1

(a,b) The water-splitting site as reported by Ferreira et al. (2004). (a) The Mn₄Ca²⁺ cluster positioned within the Mn-anomalous difference map with amino acid side chains. (b) Schematic of the amino acid ligation pattern for the model in (a) with distance less than 2.8 Å shown by connecting lines. (c,d) Remodelling the water-splitting site using the native electron density maps of Ferreira et al. (2004) and Loll et al. (2005) and Mn-anomalous difference map of Ferreira et al. (2004), keeping the Mn₃Ca²⁺O₄ cubane of Ferreira et al. but with Mn₄ linked to it via a single 3.3 Å mono-μ-oxo bridge. (c) Structure of the water-splitting site assuming a single mono-μ-oxo bridge between Mn₄ (dangler Mn) and Mn₃ of the Mn₃Ca²⁺O₄ cubane fitted into the Mn-anomalous difference map by real-space refinement using the molecular graphics program, Coot (Emsley & Cowtan 2004). The amino acid assignments and the positioning of their side chains are based on the native electron density maps of Ferreira et al. (2004) and Loll et al. (2005; see text). (d) Schematic of the amino acid ligation pattern for the model in (c) with distance less than 2.8 Å shown by connecting lines. The Mn-anomalous difference map is shown in red and contoured at 5 sigma. The arrow indicates the direction of the normal to the membrane plane.

Figure 2

A refinement of the positioning of the EXAFS models (models I, II, IIa and III) of Yano et al. (2006) into the Mn-anomalous diffraction data of Ferreira et al. (2004), maintaining the side-chain positioning given in figure 1c. Each EXAFS model was fitted by real-space refinement against the Mn-anomalous difference map of Ferreira et al. (2004) using the molecular graphics program, Coot (Emsley & Cowtan 2004). The Mn-anomalous difference map is shown in red and contoured at 5 sigma. a, c, e and g are for EXAFS models I, II, IIa and III, respectively, while b, d, f and h are the schematic for each showing potential ligation patterns where the lines represent distances of 2.8 Å or less. The arrows indicate the direction of the normal to the membrane plane.