Sequence analysis of the D1 and D2 reaction center proteins of photosystem II

A compilation of 38 sequences for the D1 and 15 sequences for the D2 reaction center proteins of photosystem II is presented. The sequences have been compared and a similarity index that takes into account the degree of conservation and the quality of the changes in each position has been calculated. The similarity index is used to identify and describe functionally important domains in the D1/D2 heterodimer. Comparative hydropathy plot are presented for the aminoacid sidechains that constitute the binding domain of the tyrosine radicals, TyrZ and TyrD, in photosystem II. The structure around TyrZ is more hydrophilic than the structure around TyrD. The hydrophilic residues are clustered in the part of the binding pocket for TyrZ that is turned towards the lumenal side of the thylakoid membrane. Most prominent is the presence of two conserved carboxylic aminoacids, D1-Asp 170 and D1-Glu 189. Their respective carboxyl-groups come close in space and are proposed to constitute a metal binding site together with D1-Gln 165. The distance between the proposed metal binding site and the center of the ring of TyrZ is approximately 7 A. The cavity that constitutes the binding site for TyrD is composed of residues from the D2 protein. Its character is more hydrophobic than the TyrZ site and the environment around TyrD lacks the cluster of putative metal binding side-chains.