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A compilation of 38 sequences for the D1 and 15 sequences for the D 2 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, Tyr Z  and Tyr D , in photosystem II. The structure around Tyr Z  is more hydrophilic than the structure around Tyr D . The hydrophilic residues are clustered in the part of the binding pocket for Tyr Z  that is turned towards the lumenal side of the thylakoid membrane. Most prominent is the presence of two conserved carboxylic am inoacids, 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 Tyr Z  is approximately 7Å . The cavity that constitutes the binding site for Tyr D  is composed of residues from the D 2 protein. Its character is more hydrophobic than the Tyr Z  site and the environment around Tyr D  lacks the cluster of putative metal binding side­-chains.

Sequence Analysis of the D1 and D2 Reaction Center Proteins of Photosystem II