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Knowledge-based modeling of the D-lactate dehydrogenase three-dimensional structure

C Vinals1, X De Bolle, E Depiereux

  • 1Facultés Universitaires Notre Dame de la Paix, Namur, Belgium.

Proteins
|April 1, 1995
PubMed
Summary

Researchers modeled the three-dimensional structure of NAD-dependent D-lactate dehydrogenase from Lactobacillus bulgaricus. The model reveals key active site residues, supporting a proposed catalytic mechanism for this enzyme.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Enzymology

Background:

  • NAD-dependent D-lactate dehydrogenase (D-LDH) is crucial in microbial metabolism.
  • Understanding its structure is key to elucidating its catalytic mechanism.
  • Lactobacillus bulgaricus D-LDH's structure has not been experimentally determined.

Purpose of the Study:

  • To generate a three-dimensional structural model of Lactobacillus bulgaricus NAD-dependent D-lactate dehydrogenase.
  • To identify potential active site residues involved in substrate binding and catalysis.
  • To support the proposed catalytic mechanism of the enzyme.

Main Methods:

  • Comparative protein modeling using the formate dehydrogenase from Pseudomonas sp. as a template.
  • Multiple sequence alignment to identify structurally conserved regions in related proteins.

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  • Knowledge-based modeling to refine the three-dimensional structure.

    • Main Results:

    • A structural model of the D-LDH subunit was generated, exhibiting an alpha/beta fold.
    • The model identified a catalytic histidine (His-296) consistent with known mechanisms.
    • Potential active site residues Arg-235 and Phe-299 were suggested for pyruvate binding and stabilization, respectively.

    Conclusions:

    • The modeled structure provides insights into the catalytic machinery of Lactobacillus bulgaricus D-LDH.
    • The findings support a hypothetical catalytic mechanism involving key active site residues.
    • This structural model serves as a basis for future experimental validation and enzyme engineering.