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Biochemistry (Moscow)

, Volume 80, Issue 13, pp 1690–1700 | Cite as

Role of a Structurally Equivalent Phenylalanine Residue in Catalysis and Thermal Stability of Formate Dehydrogenases from Different Sources

  • V. I. TishkovEmail author
  • K. V. Goncharenko
  • A. A. Alekseeva
  • S. Yu. Kleymenov
  • S. S. Savin
Review

Abstract

Comparison of amino acid sequences of NAD+-dependent formate dehydrogenases (FDH, EC 1.2.1.2) from different sources and analysis of structures of holo-forms of FDH from bacterium Pseudomonas sp. 101 (PseFDH) and soya Glycine max (SoyFDH) as well as of structure of apo-form of FDH from yeast Candida boidinii (CboFDH) revealed the presence on the surface of protein globule of hydrophobic Phe residue in structurally equivalent position (SEP). The residue is placed in the coenzyme-binding domain and protects bound NAD+ from solvent. The effects of amino acid changes of the SEP on catalytic properties and thermal stability of PseFDH, SoyFDH, and CboFDH were compared. The strongest effect was observed for SoyFDH. All eight amino acid replacements resulted in increase in thermal stability, and in seven cases, increase in catalytic constant was achieved. Thermal stability of SoyFDH after mutations Phe290Asp and Phe290Glu increased 66- and 55-fold, respectively. K M values of the enzyme for substrate and coenzyme in different cases slightly increased or decreased. In case of one CboFDH, the mutein catalytic constant increased and thermal stability did not changed. In case of the second CboFDH mutant, results were the opposite. In one PseFDH mutant, amino acid change did not influence the catalytic constant, but in three others, the parameter was reduced. Two PseFDH mutants had higher and two mutants lower thermal stability in comparison with initial enzyme. Analysis of results of SEP mutagenesis in FDHs from bacterium, yeast, and plant shows that protein structure plays a key role for effect of the same amino acid changes in equivalent position in protein globule of formate dehydrogenases from different sources.

Key words

formate dehydrogenase rational design thermal stability catalytic properties 

Abbreviations

FDH

formate dehydrogenase

PseFDH, CboFDH, and SoyFDH

recombinant formate dehydrogenases from bacterium Pseudomonas sp. 101, yeast Candida boidinii, and soy Glycine max

SEP

structurally equivalent Phe residue.

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References

  1. 1.
    Tishkov, V. I., and Popov, V. O. (2004) Catalytic mechanism and application of formate dehydrogenase, Biochemistry (Moscow), 69, 1252–1267.CrossRefGoogle Scholar
  2. 2.
    Tishkov, V. I., and Popov, V. O. (2006) Protein engineering of formate dehydrogenase, Biomol. Eng., 23, 89–110.PubMedCrossRefGoogle Scholar
  3. 3.
    Alekseeva, A. A., Savin, S. S., and Tishkov, V. I. (2011) NAD+-dependent formate dehydrogenase from plants, Acta Naturae, 3, No. 4(11), 38–54.PubMedPubMedCentralGoogle Scholar
  4. 4.
    Savin, S. S., and Tishkov, V. I. (2010) Assessment of for-mate dehydrogenase stress stability in vivo using inactiva-tion by hydrogen peroxide, Acta Naturae, 2, No. 1(4), 78–82.Google Scholar
  5. 5.
    Rojkova, A. M., Galkin, A. G., Kulakova, L. B., Serov, A. E., Savitsky, P. A., Fedorchuk, V. V., and Tishkov, V. I. (1999) Bacterial formate dehydrogenase. Increasing the enzyme thermal stability by hydrophobization of alpha helices, FEBS Lett., 445, 183–188.PubMedCrossRefGoogle Scholar
  6. 6.
    Fedorchuk, V. V., Galkin, A. G., Yasny, I. E., Kulakova, L. B., Rojkova, A. M., Filippova, A. A., and Tishkov, V. I. (2002) Influence of interactions between amino acid residues 43 and 61 on thermal stability of bacterial formate dehydrogenases, Biochemistry (Moscow), 67, 1145–1151.CrossRefGoogle Scholar
  7. 7.
    Serov, A. E., Odintzeva, E. R., Uporov, I. V., and Tishkov, V. I. (2005) Use of Ramachandran map for the increasing thermal stability of bacterial formate dehydrogenase, Biochemistry (Moscow), 70, 804–808.CrossRefGoogle Scholar
  8. 8.
    Alekseeva, A. A., Fedorchuk, V. V., Zarubina, S. A., Sadykhov, E. G., Matorin, A. D., Savin, S. S., and Tishkov, V. I. (2015) Role of Ala198 in stability and coenzyme speci-ficity of bacterial formate dehydrogenases, Acta Naturae, 7, No. 1(24), 60–69.PubMedPubMedCentralGoogle Scholar
  9. 9.
    Hofstetter, K., Lutz, J., Lang, I., Witholt, B., and Schmid, A. (2004) Coupling of biocatalytic asymmetric epoxidation with NADH regeneration in organic–aqueous emulsions, Angew. Chem. Int. Ed. Engl., 43, 2163–2166.PubMedCrossRefGoogle Scholar
  10. 10.
    Maurer, S. C., Kuehnel, K., Kaysser, L. A., Eiben, S., Schmid, R. D., and Urlacher, V. B. (2005) Catalytic hydroxylation in biphasic systems using CYP102A1 mutants, Adv. Synth. Catal., 347, 1090–1098.CrossRefGoogle Scholar
  11. 11.
    Tishkov, V. I., Galkin, A. G., Fedorchuk, V. V., Savitsky, P. A., Rojkova, A. M., Gieren, H., and Kula, M.-R. (1999) Pilot scale production and isolation of recombinant NAD+-and NADP+-specific formate dehydrogenase, Biotechnol. Bioeng., 64, 187–193.PubMedCrossRefGoogle Scholar
  12. 12.
    Alekseeva, A. A., Serenko, A. A., Kargov, I. S., Savin, S. S., Kleymenov, S. Yu., and Tishkov, V. I. (2012) Engineering catalytic properties and thermal stability of plant formate dehydrogenase by single-point mutations, Prot. Eng. Des. Select., 25, 781–788.CrossRefGoogle Scholar
  13. 13.
    Kargov, I. S., Kleymenov, S. Y., Savin, S. S., Tishkov, V. I., and Alekseeva, A. A. (2015) Improvement of the soy for-mate dehydrogenase properties by rational design, Protein Eng. Des. Sel., 28, 171–178.PubMedCrossRefGoogle Scholar
  14. 14.
    Felber, S. (2001}) Optimierung der NAD+-Abhaengigen Formiatdehydrogenase aus Candida boidinii fuer den Einsatz in der Biokatalyse: Ph. D. Thesis, Heinrich-Heine University of Duesseldorf. URL: http://diss.ub.uni-dues-seldorf.de/ebib/diss/file?dissid=78Google Scholar
  15. 15.
    Tishkov, V. I., Matorin, A. D., Rojkova, A. M., Fedorchuk, V. V., Savitsky, A. P., Dementieva, L. A., Lamzin, V. S., Mezentzev, A. V., and Popov, V. O. (1996) Site-directed mutagenesis of formate dehydrogenase active centre: role of the His332-Gln313 pair in enzyme catalysis, FEBS Lett., 390, 104–108.PubMedCrossRefGoogle Scholar
  16. 16.
    Shabalin, I. G., Polyakov, K. M., Tishkov, V. I., and Popov, V. O. (2009) Atomic resolution crystal structure of NAD+-dependent formate dehydrogenase from bacterium Moraxella sp. C-1, Acta Naturae, 1, No. 3, 89–93.Google Scholar
  17. 17.
    Tishkov, V. I., Uglanova, S. V., Fedorchuk, V. V., and Savin, S. S. (2010) Influence of ion strength and pH on thermal stability of yeast formate dehydrogenase, Acta Naturae, 2, No. 2, 82–87.Google Scholar
  18. 18.
    Sadykhov, E. G., Serov, A. E., Voinova, N. S., Uglanova, S. V., Petrov, A. S., Alexeeva, A. A., Kleimenov, S. Yu., Popov, V. O., and Tishkov, V. I. (2006) A comparable study of ther-mal stability of formate dehydrogenases from microorgan-isms and plants, Appl. Biochem. Microbiol., 42, 236–240.CrossRefGoogle Scholar
  19. 19.
    Tishkov, V. I., Popov, V. O., and Egorov, A. M. (1983) Bacterial formate dehydrogenase. Substrate specificity and kinetic mechanism of oxidation of S-formyl glutathione, Biochemistry (Moscow), 48, 1003–1010.Google Scholar
  20. 20.
    Tishkov, V. I., Galkin, A. G., and Egorov, A. M. (1989) Kinetic isotope effect and pre-steady state kinetics of the reaction catalyzed by bacterial formate dehydrogenase, Biochimie, 71, 551–557.PubMedCrossRefGoogle Scholar
  21. 21.
    Zaks, A. M., Avilova, T. V., Egorova, O. A., Popov, V. O., and Egorov, A. M. (1982) Kinetic mechanism of NAD+-depend-ent formate dehydrogenase from methylotrophic yeast Candida methylica, Biochemistry (Moscow), 47, 546–551.Google Scholar
  22. 22.
    Hermes, J. D., Morrical, S. W., O’Leary, M. H., and Cleland, W. W. (1984) Variation of transition-state structure as a function of the nucleotide in reactions catalyzed by dehydrogenases. 2. Formate dehydrogenase, Biochemistry, 23, 5479–5488.Google Scholar
  23. 23.
    Tishkov, V. I., Galkin, A. G., and Egorov, A. M. (1989) NAD-dependent formate dehydrogenase of methylotroph-ic yeast: preparation and characterization, Biochemistry (Moscow), 54, 231–237.Google Scholar
  24. 24.
    Mezentzev, A. V., Ustinnikova, T. B., Tikhonova, T. V., and Popov, V. O. (1996) Obtaining and kinetic mechanism of NAD-dependent formate dehydrogenase from methy-lotrophic yeast Hansenula polymorpha, Appl. Biochem. Microbiol. (Moscow), 32, 529–534.Google Scholar
  25. 25.
    Serov, A. E., and Tishkov, V. I. (2006) Baker’s yeast formate dehydrogenase: unusual mechanism of inactivation and stabilization by ionic strength and cofactor, Moscow Univ. Chem. Bull., 47, 1–5.Google Scholar
  26. 26.
    Alekseeva, A. A., Savin, S. S., Kleymenov, S. Yu., Uporov, I. V., Pometun, E. V., and Tishkov, V. I. (2012) Stabilization of plant formate dehydrogenase by rational design, Biochemistry (Moscow), 77, 1199–1209.CrossRefGoogle Scholar
  27. 27.
    Alekseeva, A. A., Kargov, I. S., Kleymenov, S. Yu., Savin, S. S., and Tishkov, V. I. (2015) Additivity of the stabilization effect of single amino acid substitutions in triple mutants of recombinant formate dehydrogenase from the soybean Glycine max, Acta Naturae, 7, No. 3(26), 55–64.PubMedPubMedCentralGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2015

Authors and Affiliations

  • V. I. Tishkov
    • 1
    • 2
    • 3
    Email author
  • K. V. Goncharenko
    • 1
    • 3
  • A. A. Alekseeva
    • 2
    • 3
  • S. Yu. Kleymenov
    • 2
    • 4
  • S. S. Savin
    • 1
    • 2
  1. 1.Faculty of ChemistryLomonosov Moscow State UniversityMoscowRussia
  2. 2.Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology”Russian Academy of SciencesMoscowRussia
  3. 3.Innovations and High Technologies MSU Ltd.MoscowRussia
  4. 4.Koltzov Institute of Developmental BiologyRussian Academy of SciencesMoscowRussia

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