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Related Experiment Videos

Knowledge-based modeling of a bacterial dichloromethane dehalogenase

A Marsh1, D M Ferguson

  • 1Department of Medicinal Chemistry and Minnesota Supercomputer Institute, University of Minnesota, Minneapolis 55455, USA.

Proteins
|June 1, 1997
PubMed
Summary

A structural model of dichloromethane dehalogenase (DCMD) reveals how it binds glutathione and dichloromethane. This provides insights into the enzyme's catalytic mechanism, aiding in understanding its function.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Enzymology

Background:

  • Dichloromethane dehalogenase (DCMD) from Methylophilus sp. DM11 plays a role in dehalogenation.
  • Glutathione S-transferases (GSTs) share sequence similarities with DCMD, suggesting structural homology.

Purpose of the Study:

  • To construct a three-dimensional structural model of DCMD.
  • To elucidate the structural basis for substrate binding and catalysis by DCMD.

Main Methods:

  • A hybrid approach was used to construct the DCMD model, aligning DM11 with domain I of theta class GST and domain II of alpha class GST.
  • The model was analyzed to explore substrate binding and catalytic mechanisms.

Main Results:

  • The constructed DCMD model exhibits low C alpha root mean square deviations from template GSTs.

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  • A conserved hydrogen bond network was identified for glutathione binding at the G site.
  • A proposed catalytic mechanism involves Ser12 activation and stabilization by aromatic residues His116 and Trp117.

    • Conclusions:

    • The DCMD structural model provides a basis for understanding its substrate binding and catalytic activities.
    • The proposed mechanism is consistent with experimental data and comparisons with other GSTs.