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Structural basis for the substrate specificity of 3-hydroxybutyrate dehydrogenase

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Abstract

The substrate specificity of 3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis with a non-native substrate, levulinic acid, was studied by analysis of the enzyme-substrate molecular interactions. The relation between structural and kinetic parameters was investigated considering the catalytic mechanism of the enzyme. The effects of key positive mutations (H144L, H144L/W187F) on the catalytic activity of the enzyme were studied by employing a surface analysis of its interatomic contacts between the enzyme and substrate atoms. The results revealed that the alteration of hydrogen bond network and rearrangement of the hydrophobic interactions between the active site and substrate molecule are the key structural basis for the change of the substrate specificity of 3-hydroxybutyrate dehydrogenase toward levulinic acid. With this approach, the structural basis for the substrate specificity of the enzyme could be elucidated in a quantitative manner.

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References

  1. Wohlgemuth, R. (2010) Biocatalysis-key to sustainable industrial chemistry. Curr. Opin. Biotechnol. 21: 713–724.

    Article  CAS  Google Scholar 

  2. Privett, H. K., G. Kiss, T. M. Lee, R. Blomberg, R. A. Chica, L. M. Thomas, D. Hilvert, K. N. Houk, and S. L. Mayo (2012) Iterative approach to computational enzyme design. Proc. Natl. Acad. Sci. U S A. 109: 3790–3795.

    Article  CAS  Google Scholar 

  3. Bornscheuer, U. T., G. W. Huisman, R. J. Kazlauskas, S. Lutz, J. C. Moore, and K. Robins (2012) Engineering the third wave of biocatalysis. Nature 484: 185–194.

    Article  Google Scholar 

  4. Greenhagen, B. T., P. E. O'Maille, J. P. Noel, and J. Chappell (2006) Identifying and manipulating structural determinates linking catalytic specificities in terpene synthases. Proc. Natl. Acad. Sci. U S A. 103: 9826–9831.

    Article  CAS  Google Scholar 

  5. Zhang, K., M. R. Sawaya, D. S. Eisenberg, and J. C. Liao (2008) Expanding metabolism for biosynthesis of nonnatural alcohols. Proc. Natl. Acad. Sci. U S A. 105: 20653–20658.

    Article  CAS  Google Scholar 

  6. Savile, C. K., J. M. Janey, E. C. Mundorff, J. C. Moore, S. Tam, W. R. Jarvis, J. C. Colbeck, A. Krebber, F. J. Fleitz, J. Brands, P. N. Devine, G. W. Huisman, and G. J. Hughes (2010) Biocatalytic asymmetric synthesis of chiral amines from ketones applied to sitagliptin manufacture. Sci. 329: 305–309.

    Article  CAS  Google Scholar 

  7. Yeon, Y. J., H. Y. Park, and Y. J. Yoo (2013) Enzymatic reduction of levulinic acid by engineering the substrate specificity of 3-hydroxybutyrate dehydrogenase. Bioresour. Technol. 134: 377–380.

    Article  CAS  Google Scholar 

  8. Hoque, M. M., S. Shimizu, E. C. M. Juan, Y. Sato, M. T. Hossain, T. Yamamoto, S. Imamura, K. Suzuki, H. Amano, T. Sekiguchi, M. Tsunoda, and A. Takénaka (2009) Structure of D-3-hydroxybutyrate dehydrogenase prepared in the presence of the substrate D-3-hydroxybutyrate and NAD +. Acta Crystallogr., Sect. F: Struct. Biol. Cryst. Commun. 65: 331–335.

    Article  CAS  Google Scholar 

  9. Rackemann, D. W. and W. O. Doherty (2011) The conversion of lignocellulosics to levulinic acid. Biofuels Bioprod. Biorefin. 5: 198–214.

    Article  CAS  Google Scholar 

  10. Gorenflo, V., G. Schmack, R. Vogel, and A. Steinbüchel (2001) Development of a process for the biotechnological large-scale production of 4-hydroxyvalerate-containing polyesters and characterization of their physical and mechanical properties. Biomacromol. 2: 45–57.

    Article  CAS  Google Scholar 

  11. Horváth, I. T., H. Mehdi, V. Fábos, L. Boda, and L. T. Mika (2008) γ-Valerolactone-a sustainable liquid for energy and carbon-based chemicals. Green Chem. 10: 238–242.

    Article  Google Scholar 

  12. Hoque, M. M., S. Shimizu, M. T. Hossain, T. Yamamoto, S. Imamura, K. Suzuki, M. Tsunoda, H. Amano, T. Sekiguchi, and A. Takénaka (2008) The structures of Alcaligenes faecalis D-3-hydroxybutyrate dehydrogenase before and after NAD+ and acetate binding suggest a dynamical reaction mechanism as a member of the SDR family. Acta Crystallogr. Sect. D: Biol. Crystallogr. 64: 496–505.

    Article  CAS  Google Scholar 

  13. Hoque, M. M., S. Shimizu, E. C. M. Juan, Y. Sato, M. T. Hossain, T. Yamamoto, S. Imamura, K. Suzuki, H. Amano, T. Sekiguchi, M. Tsunoda, and A. Takénaka (2009) Structure of D-3-hydroxybutyrate dehydrogenase prepared in the presence of the substrate D-3-hydroxybutyrate and NAD+. Acta Crystallogr. Sect. F: Struct. Biol. Cryst. Commun. 65: 331–335.

    Article  CAS  Google Scholar 

  14. Basner, J. E. and S. D. Schwartz (2004) Donor-acceptor distance and protein promoting vibration coupling to hydride transfer: A possible mechanism for kinetic control in isozymes of human lactate dehydrogenase. J. Phys. Chem. B. 108: 444–451.

    Article  CAS  Google Scholar 

  15. Pudney, C. R., L. O. Johannissen, M. J. Sutcliffe, S. Hay, and N. S. Scrutton (2010) Direct analysis of donor-acceptor distance and relationship to isotope effects and the force constant for barrier compression in enzymatic H-tunneling reactions. J. Am. Chem. Soc. 132: 11329–11335.

    Article  CAS  Google Scholar 

  16. Stojkovi, V., L. L. Perissinotti, D. Willmer, S. J. Benkovic, and A. Kohen (2012) Effects of the donor-acceptor distance and dynamics on hydride tunneling in the dihydrofolate reductase catalyzed reaction. J. Am. Chem. Soc. 134: 1738–1745.

    Article  Google Scholar 

  17. Vasavada, M., C. E. Carpenter, D. P. Cornforth, and V. Ghorpade (2003) Sodium levulinate and sodium lactate effects on microbial growth and stability of fresh pork and turkey sausages. J. Muscle Foods. 14: 119–129.

    Article  CAS  Google Scholar 

  18. Zheng, L., U. Baumann, and J. L. Reymond (2004) An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res. 32: e115.

    Article  Google Scholar 

  19. Kim, S. H., S. Pokhrel, and Y. J. Yoo (2008) Mutation of non-conserved amino acids surrounding catalytic site to shift pH optimum of Bacillus circulans xylanase. J. Mol. Catal. B: Enz. 55: 130–136.

    Article  CAS  Google Scholar 

  20. Bradford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein dye binding. Anal. Biochem. 72: 248–254.

    Article  CAS  Google Scholar 

  21. Clark, M., R. D. Cramer, and N. Van Opdenbosch (1989) Validation of the general purpose tripos 5.2 force field. J. Comput. Chem. 10: 982–1012.

    Article  CAS  Google Scholar 

  22. Purcell, W. P. and J. A. Singer (1967) A brief review and table of semiempirical parameters used in the Hueckel molecular orbital method. J. Chem. Eng. Data. 12: 235–246.

    Article  CAS  Google Scholar 

  23. Lovell, S. C., J. M. Word, J. S. Richardson, and D. C. Richardson (2000) The penultimate rotamer library. Proteins: Struct. Funct. Bioinf. 40: 389–408.

    Article  CAS  Google Scholar 

  24. Jain, A. N. (2003) Surflex: Fully Automatic flexible molecular docking using a molecular similarity-based search engine. J. Med. Chem. 46: 499–511.

    Article  CAS  Google Scholar 

  25. Sobolev, V., A. Sorokine, J. Prilusky, E. E. Abola, and M. Edelman (1999) Automated analysis of interatomic contacts in proteins. Bioinformat. 15: 327–332.

    Article  CAS  Google Scholar 

  26. Yeon, Y. J., H. J. Park, H. Y. Park, and Y. J. Yoo (2014) Effect of His-tag location on the catalytic activity of 3-hydroxybutyrate dehydrogenase. Biotechnol. Bioproc. Eng. 19: 798–802.

    Article  CAS  Google Scholar 

  27. Kamerlin, S. C. L. and A. Warshel (2010) At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis. Proteins: Struct. Funct. Bioinformat. 78: 1339–1375.

    CAS  Google Scholar 

  28. Bhabha, G., J. Lee, D. C. Ekiert, J. Gam, I. A. Wilson, H. J. Dyson, S. J. Benkovic, and P. E. Wright (2011) A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Sci. 332: 234–238.

    Article  CAS  Google Scholar 

  29. Park, J. C., J. C. Joo, E. S. An, B. K. Song, Y. H. Kim, and Y. J. Yoo (2011) A combined approach of experiments and computational docking simulation to the Coprinus cinereus peroxidasecatalyzed oxidative polymerization of alkyl phenols. Bioresour. Technol. 102: 4901–4904.

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. The Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Korea

    Young Joo Yeon

  2. School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Korea

    Young Joo Yeon & Young Je Yoo

  3. Bio-MAX Institute, Seoul National University, Seoul, 08826, Korea

    Hyung-Yeon Park, Hyun June Park & Young Je Yoo

  4. Department of Biological and Chemical Engineering, Hongik University, Sejong, 30016, Korea

    Kyungmoon Park

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  1. Young Joo Yeon
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  2. Hyung-Yeon Park
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  5. Young Je Yoo
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Correspondence to Young Je Yoo.

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Yeon, Y.J., Park, HY., Park, K. et al. Structural basis for the substrate specificity of 3-hydroxybutyrate dehydrogenase. Biotechnol Bioproc E 21, 364–372 (2016). https://doi.org/10.1007/s12257-016-0233-2

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  • DOI: https://doi.org/10.1007/s12257-016-0233-2

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