Journal of Protein Chemistry

, Volume 11, Issue 2, pp 139–155 | Cite as

Structural domains of phytochrome deduced from homologies in amino acid sequences

  • Marek Romanowski
  • Pill-Soon Song


A method of semiempirical identification of structural domains is proposed. The procedure is based on the comparison of amino acid sequences in groups of homologous proteins. This approach was tested using 32 known protein sequences from different cytochromeb5, cytochromec, lysozyme, hemoglobin, and myoglobin proteins. The method presented was able to identify all structural domains of these reference proteins. A consensus secondary structure provided information on structural content of these domains predicting correctly 21 of 23 (91%) of α-helices. We applied this method to six homologous phytochrome sequences fromAvena, Arabadopsis, Cucurbita, Maize, Oryza, andPisum. Some of the identified domains can be assigned to the known tertiary structure categories. For example, an α/β domain is localized in the region known to stabilize the phytochrome chromophore in the red light absorbing form (Pr). One α-helical and one α/β domains are localized in regions important for the chromophore stabilization in the far-red absorbing form (Pfr). From an analysis of noncovalent interaction patterns in another domain it is proposed that a phytochrome dimer contact involves two segments localized between residues 730 and 821 (using numbering of aligned sequences). Also, a possible antiparallel β-sheet structure of this region has been suggested. According to this model, the long axis of the interacting structures is perpendicular to a twofold symmetry axis of the phytochrome dimer.

Key words

Phytochrome protein homology protein domains peptide conformation signal transduction photomorphogenesis 


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Copyright information

© Plenum Publishing Corporation 1992

Authors and Affiliations

  • Marek Romanowski
    • 1
  • Pill-Soon Song
    • 1
  1. 1.Department of Chemistry and Institute for Cellular and Molecular PhotobiologyUniversity of NebraskaLincoln

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