A three-dimensional model of the Photosystem II reaction centre of Pisum sativum

A three-dimensional model of the core proteins D1 and D2, including the cofactors, that form the Photosystem II reaction centre of pea (Pisum sativum), has been generated. This model was built with a rule-based computer modelling system using the information from the crystal structures of the photosynthetic reaction centres of Rhodopseudomonas viridis and Rhodobacter sphaeroides. An alignment of the primary sequences of twenty three D1, nine D2, eight bacterial L and eight bacterial M subunits predicts strong similarity between bacterial and higher plant reaction centres, especially in the transmembrane region where the cofactors responsible for electron transport are located. The sequence to be modelled was aligned to the bacterial structures using environment-dependent substitution tables to construct matrices, improving the alignment procedure. The ancestral relationship between the bacteria and higher plant sequences allowed both the L and M subunits to be used as structural templates as they were equally related to the higher plant polypeptides. The regions with the highest predicted structural homology were used as a framework for the construction of the structurally conserved regions. The structurally conserved region of the model shows strong similarity to the bacterial reaction centre in the transmembrane helices. The stromal and lumenal loops show greater sequence variation and are therefore predicted to be the structurally variable regions in the model. The key sidechain assignments and residues that may interact with cofactors are discussed.