Journal of Molecular Evolution

, Volume 50, Issue 1, pp 39–44 | Cite as

Phylogeny of the Restriction Endonuclease-Like Superfamily Inferred from Comparison of Protein Structures

  • Janusz M.  Bujnicki


To date all attempts to derive a phyletic relationship among restriction endonucleases (ENases) from multiple sequence alignments have been limited by extreme divergence of these enzymes. Based on the approach of Johnson et al. (1990), I report for the first time the evolutionary tree of the ENase-like protein superfamily inferred from quantitative comparison of atomic coordinates of structurally characterized enzymes. The results presented are in harmony with previous comparisons obtained by crystallographic analyses. It is shown that λ-exonuclease initially diverged from the common ancestor and then two ``endonucleolytic'' families branched out, separating ``blunt end cutters'' from ``5′ four-base overhang cutters.'' These data may contribute to a better understanding of ENases and encourage the use of structure-based methods for inference of phylogenetic relationship among extremely divergent proteins. In addition, the comparison of three-dimensional structures of ENase-like domains provides a platform for further clustering analyses of sequence similarities among different branches of this large protein family, rational choice of homology modeling templates, and targets for protein engineering.

Key words: Restriction endonucleases — Divergent evolution — Distance matrix methods — Phyletic trees from X-ray crystal structures — Target recognition — Remote homology 


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Copyright information

© Springer-Verlag New York Inc. 2000

Authors and Affiliations

  • Janusz M.  Bujnicki
    • 1
  1. 1.Molecular Biology Research Program. Henry Ford Health System, One Ford Place, Suite 5D, Detroit, MI 48202, USAUS

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