Modeling of pyruvate decarboxylases from ethanol producing bacteria




Anjala Shrestha1, Srisuda Dhamwichukorn1, 2, Ekachai Jenwitheesuk3, 4*



1Joint Graduate School of Energy and Environment, King Mongkut’s University of Technology Thonburi, Prachautid Road, Toongkru, Bangkok 10140, Thailand; 2Pacific Time Co., Ltd. 77/123 Sinn Sathorn Tower, 29th Floor. Krungthonburi Road. Kongton sai, Klongsan, Bangkok 10600, Thailand; 3Bioinformatics program, King Mongkut’s University of Technology Thonburi, Prachautid Road, Toongkru, Bangkok 10140, Thailand; 4National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klongluang, Pathumthani 12120, Thailand.



Article Type





Received May 25, 2009; Revised December 19, 2009; Accepted February 10, 2010; Published February 28, 2010



Pyruvate decarboxylase (PDC) is a key enzyme in homoethanol fermentation process, which decarboxylates 2-keto acid pyruvate into acetaldehyde and carbon dioxide. PDC enzymes from potential ethanol-producing bacteria such as Zymomonas mobilis, Zymobacter palmae and Sarcina ventriculi have different Km and kcat values for the substrate pyruvate at their respective optimum pH. In this study, the putative three-dimensional structures of PDC dimer of Z. palmae PDC and S. ventriculi PDC were generated based on the X-ray crystal structures of Z. mobilis PDC, Saccharomyces cerevisiae PDC form-A and Enterobacter cloacae indolepyruvate decarboxylase in order to compare the quaternary structures of these bacterial PDCs with respect to enzyme-substrate interactions, and subunit-subunit interfaces that might be related to the different biochemical characteristics. The PROCHECK scores for both models were within recommended intervals. The generated models are similar to the X-ray crystal structure of Z. mobilis PDC in terms of binding modes of the cofactor, the position of Mg2+, and the amino acids that form the active sites. However, subunit-subunit interface analysis showed lower H-bonding in both models compared with X-ray crystal structure of Z. mobilis PDC, suggesting a smaller interface area and the possibility of conformational change upon substrate binding in both models. Both models have predicted lower affinity towards branched and aromatic 2-keto acids, which correlated with the molecular volumes of the ligands. The models shed valuable information necessary for further improvement of PDC enzymes for industrial production of ethanol and other products.



bacterial pyruvate decarboxylase; homology modelling; molecular docking, 2- keto acids.




Shrestha et al, Bioinformation 4(8): 378-384 (2010)

Edited by


P. Kangueane








Biomedical Informatics




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