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Related Experiment Videos

Evolution of function in protein superfamilies, from a structural perspective.

A E Todd1, C A Orengo, J M Thornton

  • 1Biochemistry and Molecular Biology Department, University College London, Gower Street, London, WC1E 6BT, UK.

Journal of Molecular Biology
|April 5, 2001
PubMed
Summary

Protein superfamilies show significant functional diversity, with variations in enzyme type and substrate specificity common. Structural data is crucial for understanding function in distantly related proteins.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Protein databases reveal extensive functional diversity within protein superfamilies.
  • Homologous enzyme superfamilies, classified by CATH, exhibit varied enzymatic functions.

Purpose of the Study:

  • Assess functional variation in homologous enzyme superfamilies using the Enzyme Commission (EC) scheme.
  • Investigate mechanisms of functional diversity generation during evolution.

Main Methods:

  • Combined sequence and structure information to identify protein relatives.
  • Analyzed 486,000 homologous pairs across varying sequence identities.
  • Detailed study of 31 diverse structural enzyme superfamilies.

Main Results:

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  • Majority of superfamilies display functional variation; 25% have members of different enzyme types.
  • Functional variation is rare above 40% sequence identity; EC number prediction accurate above 30%.
  • Below 30% sequence identity, structural data is essential for understanding functional differences; local sequence variation and domain shuffling are key diversity mechanisms.

Conclusions:

  • Functional diversity within enzyme superfamilies is widespread and generated through various evolutionary mechanisms.
  • Substrate specificity often varies, while reaction chemistry is generally conserved.
  • Understanding this diversity is critical for structural genomics projects.