Journal of Molecular Evolution

, Volume 54, Issue 1, pp 17–29

Classification and Phylogenetic Analysis of the cAMP-Dependent Protein Kinase Regulatory Subunit Family

  • Jaume M.  Canaves
  • Susan S.  Taylor

DOI: 10.1007/s00239-001-0013-1

Cite this article as:
Canaves, J. & Taylor, S. J Mol Evol (2002) 54: 17. doi:10.1007/s00239-001-0013-1

Abstract.

The members of the PKA regulatory subunit family (PKA-R family) were analyzed by multiple sequence alignment and clustering based on phylogenetic tree construction. According to the phylogenetic trees generated from multiple sequence alignment of the complete sequences, the PKA-R family was divided into four subfamilies (types I to IV). Members of each subfamily were exclusively from animals (types I and II), fungi (type III), and alveolates (type IV). Application of the same methodology to the cAMP-binding domains, and subsequently to the region delimited by β-strands 6 and 7 of the crystal structures of bovine RIα and rat RIIβ (the phosphate-binding cassette; PBC), proved that this highly conserved region was enough to classify unequivocally the members of the PKA-R family. A single signature sequence, F–G–E–[LIV]–A–L–[LIMV]–x(3)–[PV]–R–[ANQV]–A, corresponding to the PBC was identified which is characteristic of the PKA-R family and is sufficient to distinguish it from other members of the cyclic nucleotide-binding protein superfamily. Specific determinants for the A and B domains of each R-subunit type were also identified. Conserved residues defining the signature motif are important for interaction with cAMP or for positioning the residues that directly interact with cAMP. Conversely, residues that define subfamilies or domain types are not conserved and are mostly located on the loop that connects α-helix B′ and β strand 7.

Key words: PKA — cAMP — cAPK — Regulatory subunit — Motif — Classification — Phylogeny — Signature 

Copyright information

© Springer-Verlag New York Inc. 2002

Authors and Affiliations

  • Jaume M.  Canaves
    • 1
  • Susan S.  Taylor
    • 1
  1. 1.Department of Chemistry and Biochemistry, 0654, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0654, USAUS

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