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Related Experiment Videos

Structure-based sequence alignment of type-II restriction endonucleases.

T Deva1, S Krishnaswamy

  • 1Bioinformatics Center, School of Biotechnology, Madurai Kamaraj University, 625 021, Madurai, India.

Biochimica Et Biophysica Acta
|May 9, 2001
PubMed
Summary

Despite low sequence identity, type-II restriction enzymes share structural similarities. New sequence motifs were identified, aiding in understanding DNA binding and active sites for these crucial enzymes.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biology

Background:

  • Type-II restriction endonucleases typically lack significant amino acid sequence homology.
  • Despite low sequence identity (<23%), crystal structures reveal striking 3D-structural resemblance between EcoRI and BamHI, including similar folds and active sites.

Purpose of the Study:

  • To identify conserved sequence motifs in type-II restriction endonucleases despite overall low sequence homology.
  • To investigate the functional implications of these motifs in DNA binding, active site formation, and dimer formation.

Main Methods:

  • Structural superimposition of restriction endonucleases (EcoRI, BamHI, EcoRV, PvuII) based on active site residues.
  • Sequence alignment to identify nine potential sequence motifs.

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  • Modified profile analysis to identify similar regions in uncharacterized endonuclease sequences.

    • Main Results:

    • Nine sequence motifs were identified, characterized by charged and/or hydrophobic residues.
    • Motifs were implicated in DNA binding (3), active site formation (3), and dimer formation (1).
    • Specific motifs (e.g., motif IX, motif III/PD motif) showed variations in sequence order and relatedness, suggesting subgroup differences.

    Conclusions:

    • Conserved sequence motifs can be identified in type-II restriction endonucleases through structure-guided alignment, even with low sequence identity.
    • These motifs provide insights into the functional regions of these enzymes.
    • Modified profile analysis successfully identified similar regions in related endonucleases lacking known structures.