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Modeling of pyruvate decarboxylases from ethanol producing bacteria
Anjala Shrestha1, Srisuda Dhamwichukorn, Ekachai Jenwitheesuk
1Joint Graduate School of Energy and Environment, King Mongkut’s University of Technology Thonburi, Prachautid Road, Toongkru, Bangkok 10140, Thailand.
Bioinformation
|October 27, 2010
Summary
Pyruvate decarboxylase (PDC) structural models reveal differences in subunit interactions and substrate affinity. These findings offer insights for enhancing PDC enzymes for industrial ethanol production.
Area of Science:
- Biochemistry and Structural Biology
- Enzymology
- Metabolic Engineering
Background:
- Pyruvate decarboxylase (PDC) is crucial for homoethanol fermentation, converting pyruvate to acetaldehyde and CO2.
- Bacterial PDCs from Zymomonas mobilis, Zymobacter palmae, and Sarcina ventriculi exhibit varying kinetic properties (Km, kcat) at different optimal pH.
- Understanding structural variations in PDC is key to optimizing ethanol production.
Purpose of the Study:
- To generate and compare the three-dimensional structures of Z. palmae PDC and S. ventriculi PDC dimers.
- To analyze quaternary structures, enzyme-substrate interactions, and subunit interfaces of bacterial PDCs.
- To relate structural findings to observed biochemical differences and guide enzyme engineering for industrial applications.
Main Methods:
- Homology modeling was used to generate putative 3D structures of Z. palmae PDC and S. ventriculi PDC dimers.
- Models were based on X-ray crystal structures of related enzymes (Z. mobilis PDC, S. cerevisiae PDC, E. cloacae ICDH).
- Structural analysis included PROCHECK validation, active site comparison, cofactor binding, Mg2+ positioning, and subunit interface analysis.
Main Results:
- Generated PDC models showed structural similarity to Z. mobilis PDC regarding cofactor binding, Mg2+ site, and active site amino acids.
- Subunit interface analysis revealed reduced H-bonding in Z. palmae and S. ventriculi PDC models compared to Z. mobilis PDC, suggesting smaller interfaces.
- Models predicted lower affinity for branched and aromatic 2-keto acids, correlating with ligand molecular volumes.
Conclusions:
- Structural models highlight potential conformational flexibility in Z. palmae and S. ventriculi PDCs upon substrate binding.
- Differences in subunit interfaces may explain variations in biochemical characteristics among bacterial PDCs.
- The study provides valuable structural insights for the rational design and improvement of PDC enzymes for industrial ethanol and other product biosynthesis.
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