Threading structural model of the manganese‐stabilizing protein PsbO reveals presence of two possible β‐sandwich domains

Abstract

The manganese-stabilizing protein (PsbO) is an essential component of photosystem II (PSII) and is present in all oxyphotosynthetic organisms. PsbO allows correct water splitting and oxygen evolution by stabilizing the reactions driven by the manganese cluster. Despite its important role, its structure and detailed functional mechanism are still unknown. In this article we propose a structural model based on fold recognition and molecular modeling. This model has additional support from a study of the distribution of characteristics of the PsbO sequence family, such as the distribution of conserved, apolar, tree-determinants, and correlated positions. Our threading results consistently showed PsbO as an all-beta (beta) protein, with two homologous beta domains of approximately 120 amino acids linked by a flexible Proline-Glycine-Glycine (PGG) motif. These features are compatible with a general elongated and flexible architecture, in which the two domains form a sandwich-type structure with Greek key topology. The first domain is predicted to include 8 to 9 beta-strands, the second domain 6 to 7 beta-strands. An Ig-like beta-sandwich structure was selected as a template to build the 3-D model. The second domain has, between the strands, long-loops rich in Pro and Gly that are difficult to model. One of these long loops includes a highly conserved region (between P148 and P174) and a short alpha-helix (between E181 and N188)). These regions are characteristic parts of PsbO and show that the second domain is not so similar to the template. Overall, the model was able to account for much of the experimental data reported by several authors, and it would allow the detection of key residues and regions that are proposed in this article as essential for the structure and function of PsbO.

Crystal structure of oxygen-evolving photosystem II fromThermosynechococcus vulcanusat 3.7-Å resolution

“…Arrowheads indicate two chls, one in CP47 and one in CP43, found in the present structure but not in the structure of T. elongatus (44), whereas a rectangle indicates a chl found in CP43 in T. elongatus's structure but not in the present structure (view from the luminal side perpendicular to the membrane plane). compatible with the model predicted theoretically (38) or that analyzed by single-particle analysis of cryoelectron microscopic images from higher plants (39). The structure of cyt c550 was modeled partially with the help of the recently reported structure of this cyt from two other cyanobacteria (40,41), generating a structure very similar to those from the other cyanobacteria.…”

Three-dimensional Electron Cryo-microscopy Study of the Extrinsic Domains of the Oxygen-evolving Complex of Spinach

“…Protein Structural Predictions and Threading-A structural model of PsbO has been obtained (14). This model was constructed based on remote homology using a protocol that follows three progressive criteria for a correct assignment: 1) reliability and consistency of fold recognitions obtained using seven different threading methods (TOPITS, GONPM, H3P2, 3-PSSM, HFR, THREADER2, and HMM); 2) quantitative evaluation of the fitting of the different Protein Data Bank templates selected to the internal properties of the target protein, PsbO (the properties studied were: clustering of apolar residues, clustering of conserved residues, and conservation of correlated residues and of treedeterminant amino acids); and 3) consistency or agreement of the predicted model with experimental data known about the structure of the protein.…”

“…Finally, experimental structural data that are available for PsbO were used to recheck the model. The basic principles of each threading method used and full details of the PsbO fold recognition and model construction are detailed in Pazos et al (14) RESULTS…”

“…We have refined the density map of the spinach PSII supercomplex to 17 Å, and in this study, the data are presented with special focus on the region assigned to the PsbO protein on the lumenal side of PSII. The results obtained are discussed in terms of structural predictions for the PsbO protein based on computational methodologies (14) and the x-ray structure of cyanobacterial PSII published recently in Ref. 16.…”

“…Fourier transform infrared spectroscopy has indicated that the 33-kDa protein is composed predominantly of ␤-structure (7-10), a conclusion reinforced by circular dichroism (CD) measurements in the ultraviolet region (11,12). Structural predictions also suggest that this is a ␤-protein consisting of nine or more ␤-strands with a high proportion of loops and turns (6,13,14). These predictions have recently been used to assign a region of the x-ray-derived map of the PSII core of Synechococcus elongatus to a portion of the PsbO protein (15) Less is known about the structure of the PsbP and PsbQ extrinsic OEC proteins present in higher plants and algae (5).…”