Structural domains of phytochrome deduced from homologies in amino acid sequences

Marek Romanowski, Pill Soon Song

Research output: Contribution to journalArticlepeer-review


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 cytochrome b5, cytochrome c, 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 from Avena, Arabadopsis, Cucurbita, Maize, Oryza, and Pisum. 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.

Original languageEnglish (US)
Pages (from-to)139-155
Number of pages17
JournalJournal of Protein Chemistry
Issue number2
StatePublished - Apr 1992


  • Phytochrome
  • peptide conformation
  • photomorphogenesis
  • protein domains
  • protein homology
  • signal transduction

ASJC Scopus subject areas

  • Biochemistry


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