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Understanding structural/functional properties of amidase from Rhodococcus erythropolis by computational approaches

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Abstract

The 3D structure of the amidase from Rhodococcus erythropolis (EC 3.5.1.4) built by homology-based modeling is presented. Propionamide and acetamide are docked to the amidase. The reaction models were used to characterize the explicit enzymatic reaction. The calculated free energy barrier at B3LYP/6-31G* level of Model A (Ser194 + propionamide) is 19.72 kcal mol−1 in gas (6.47 kcal mol−1 in solution), and of Model B (Ser194 + Gly193 + propionamide) is 18.71 kcal mol−1 in gas (4.57 kcal mol−1 in solution). The docking results reveal that propionamide binds more strongly than acetamide due to the ethyl moiety of propionamide, which makes the carboxyl oxygen center of the substrate slightly more negative, making formation of the positively charged tetrahedral intermediate slightly easier. The quantum mechanics results demonstrate that Ser194 is essential for the acyl-intermediate, and Gly193 plays a secondary role in stabilizing acyl-intermediate formation as the NH groups of Ser194 and Gly193 form hydrogen bonds with the carbonyl oxygen of propionamide. The new structural and mechanistic insights gained from this computational study should be useful in elucidating the detailed structures and mechanisms of amidase and other homologous members of the amidase signature family.

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Acknowledgments

This work was supported by the National Science Foundation of China (20333050, 20673044), Doctor Foundation by the Ministry of Education, and Foundation for University Key Teacher by the Ministry of Education, Key subject of Science and Technology by the Ministry of Education of China, and Key subject of Science and Technology by Jilin Province.

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Authors and Affiliations

  1. Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun, 130023, People’s Republic of China

    Wei-Wei Han, Ying Wang, Yi-Han Zhou, Yuan Yao & Ze-Sheng Li

  2. The Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, 130023, People’s Republic of China

    Wei-Wei Han & Yan Feng

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  1. Wei-Wei Han
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  2. Ying Wang
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  3. Yi-Han Zhou
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  4. Yuan Yao
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  6. Yan Feng
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Correspondence to Ze-Sheng Li or Yan Feng.

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Han, WW., Wang, Y., Zhou, YH. et al. Understanding structural/functional properties of amidase from Rhodococcus erythropolis by computational approaches. J Mol Model 15, 481–487 (2009). https://doi.org/10.1007/s00894-008-0406-9

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  • DOI: https://doi.org/10.1007/s00894-008-0406-9

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