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Modeling an Enzyme Active Site using Molecular Visualization Freeware
Published on: December 25, 2021
Using catalytic atom maps to predict the catalytic functions present in enzyme active sites.
1Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States.
Biochemistry
|August 23, 2012
Summary
Catalytic atom maps (CAMs) accurately identify enzyme active sites by analyzing residue microenvironments. This method successfully predicted catalytic functions across diverse protein structures.
Area of Science:
- Biochemistry
- Structural Biology
- Enzymology
Background:
- Enzyme active sites contain catalytic residues crucial for function.
- Catalytic atom maps (CAMs) offer simplified models of these active sites.
- The relationship between active site geometry and catalytic function requires further investigation.
Purpose of the Study:
- To determine if similar geometries in enzyme active sites correlate with identical catalytic functions.
- To develop and validate a computational method for identifying enzyme active sites based on CAMs and residue microenvironment.
- To explore the catalytic functionality of orotidine 5 omino-monophosphate decarboxylase (ODCase).
Main Methods:
- Utilized the Protein Data Bank (PDB) to analyze protein structures.
- Developed a CAM-based search protocol combined with a weighted contact number (WCN) filter.
- Applied CAMs to identify known catalytic triads (Ser-His-Asp) and Cys-Arg-(Asp/Glu) motifs with high accuracy.
- Searched for ODCase-like active sites using a CAM based on its conserved tetrad.
Main Results:
- A trypsin-based CAM identified catalytic triads with 96% accuracy (0.5 Å rmsd).
- A tyrosine phosphatase-based CAM achieved 89% accuracy in identifying similar active sites.
- CAMs successfully identified active sites across different protein fold types.
- The ODCase CAM revealed structural similarities to Schiff base-forming Class I aldolases (0.48 Å rmsd).
Conclusions:
- CAMs combined with WCN analysis are effective for identifying enzyme active sites and predicting catalytic function.
- The study suggests ODCase may utilize a catalytic mechanism involving nucleophilic lysine generation, similar to aldolases.
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