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Related Experiment Videos

Superfamily active site templates.

Elaine C Meng1, Benjamin J Polacco, Patricia C Babbitt

  • 1Department of Pharmaceutical Chemistry, University of California, Genentech Hall, 600 Sixteenth Street, San Francisco, CA 94143-2240, USA.

Proteins
|May 18, 2004
PubMed
Summary

Three-dimensional protein signatures, or templates, accurately identify enzyme superfamily members. This method focuses on conserved functional residues, offering greater specificity than fold similarity alone for classifying enzymes.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Enzyme superfamilies exhibit diverse catalytic functions despite shared ancestry.
  • Classifying enzymes into superfamilies is crucial for understanding protein function and evolution.
  • Current methods often rely on overall structural similarity, which can be insufficient for diverse superfamilies.

Purpose of the Study:

  • To develop and validate a method for identifying enzyme superfamily members using three-dimensional functional signatures.
  • To demonstrate the efficacy of active site templates for superfamily classification.
  • To explore the general applicability of this approach across different enzyme folds.

Main Methods:

  • Utilized three-dimensional signatures composed of key functional residues.

Related Experiment Videos

  • Applied active site templates to identify members of the enolase superfamily in structural databases.
  • Tested the method's sensitivity and specificity in comparison to fold similarity searches.
  • Examined preliminary results for the haloacid dehalogenase superfamily.

    • Main Results:

    • Three-dimensional signatures accurately identified enolase superfamily members with high sensitivity and specificity.
    • The template-based approach proved more specific than fold similarity for distinguishing superfamilies within the (beta/alpha)8 barrel fold.
    • Functional signatures captured conserved chemical capabilities, unifying diverse enzyme reactions within superfamilies.
    • Preliminary data suggests broad applicability to other enzyme families, like haloacid dehalogenases.

    Conclusions:

    • Functional residue signatures provide a powerful and specific means for enzyme superfamily classification.
    • This method enhances the ability to assign function to unknown proteins based on conserved active site characteristics.
    • The approach offers a valuable tool for protein classification and functional inference in structural biology and bioinformatics.