The complete amino acid sequence of the alpha subunit of phycocyanin from the unicellular rhodophyte Cyanidium caldarium has been determined by automated sequential degradation of cyanogen bromide peptides, tryptic peptides derived from protein chemically modified with 1,2-cyclohexanedione or citraconic anhydride, and a peptide obtained after cleavage of the protein at the single tryptophan residue. The alpha subunit contains 162 amino acids and methionine and serine are the NH2- and carboxyl-terminal amino acids, respectively. The calculated molecular weight of the protein, based on the amino acid sequence, is 18,303, in good agreement with the value of 17,500 +/- 500, obtained by electrophoresis on calibrated sodium dodecyl sulfate-polyacrylamide gels. One phycocyanobilin chromophore is attached to the alpha subunit at residue 84 by a cysteinyl thioether linkage. A second cysteine (residue 98) is present but is not linked to phycocyanobilin. The amino acid sequence of the alpha subunit of phycocyanin from C. caldarium is the first complete amino acid sequence of a phycobiliprotein from a eukaryotic alga. Extensive homology occurs between the alpha subunit of phycocyanin from C. caldarium and from two prokaryotic cyanobacteria, and the significance of this is discussed.
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