Abstract
NAD+-dependent formate dehydrogenase (EC 1.2.1.2, FDH) from pathogenic bacterium Staphylococcus aureus (SauFDH) differs significantly from other FDHs both in terms of primary structure and catalytic properties. A distinctive feature of SauFDH is the highest (about 2.5–3 times) specific activity compared to other formate dehydrogenases. At the same time, SauFDH has high Michaelis constants for both substrates. Based on the analysis of three-dimensional structures and the alignment of amino acid sequences, replacements promising in terms of changing catalytic parameters were selected. The replacement of I220H resulted in an increase in \(K_{{\text{M}}}^{{{\text{NA}}{{{\text{D}}}^{{\text{ + }}}}}}\); the value of kcat has not changed. When T250H is replaced, an increase in \(K_{{\text{M}}}^{{{\text{NA}}{{{\text{D}}}^{{\text{ + }}}}}}\) is observed, kcat decreases from 20 to 13 s–1. The replacement of K368H led to a slight increase in \(K_{{\text{M}}}^{{{\text{NA}}{{{\text{D}}}^{{\text{ + }}}}}}\), kcat decreased from 20 to 6 s–1. The introduction of TGA and AGA additional inserts in α-helix at the C-terminus of the enzyme led to an increase in \(K_{{\text{M}}}^{{{\text{NA}}{{{\text{D}}}^{{\text{ + }}}}}}\) and \(K_{{\text{M}}}^{{{\text{HCO}}{{{\text{O}}}^{ - }}}}\). A bigger effect was observed for \(K_{{\text{M}}}^{{{\text{NA}}{{{\text{D}}}^{{\text{ + }}}}}}\)—the difference was more than 10 times. For mutant SauFDH with insertions kcat significantly reduced to 4 s–1. Similar results were observed for mutants with multipoint replacements. Thus, the C-terminal sequence has been shown to play an important role in the catalysis of SauFDH.
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REFERENCES
Tishkov, V.I. and Popov, V.O., Biochemistry (Moscow), 2004, vol. 69, no. 11, p. 1252. https://doi.org/10.1007/s10541-005-0071-x
Tishkov, V.I. and Popov, V.O., Biomol. Eng., 2006, vol. 23, p. 89. https://doi.org/10.1016/j.bioeng.2006.02.003
Alekseeva, A.A., Savin, S.S., and Tishkov, V.I., Acta Nat., 2011, vol. 3, no. 4, p. 38. https://doi.org/10.32607/20758251-2011-3-4-38-54
Resch, A., Rosenstein, R., Nerz, C., and Götz, F., Appl. Environ. Microbiol., 2005, vol. 71, no. 5, p. 2663.
Tishkov, V.I., Goncharenko, K.V., Alekseeva, A.A., Kleymenov, S.Yu., and Savin, S.S., Biochemistry (Moscow), 2015, vol. 80, no. 13, p. 1690.
Ernst, M., Kaup, B., Muller, M., Bringer-Meyer, S., and Sahm, H., Appl. Microbiol. Biotechnol., 2005, vol. 66, no. 6, p. 629.
Weckbecker, A., Groger, H., and Hummel, W., Adv. Biochem. Eng. Biotechnol., 2010, vol. 120, p. 195.
Liu, Q., Zhou, J., Yang, T., Zhang, X., Xu, M., and Rao, Z., Appl. Microbiol. Biotechnol., 2018, vol. 102, no. 5, p. 2129.
Tishkov, V.I., Pometun, A.A., Stepashkina, A.V., Fedorchuk, V.V., Zarubina, S.A., Kargov, I.S., Atroshenko, D.L., Parshin, P.D., Shelomov, M.D., Kovalevski, R.P., Boiko, K.M., Eldarov, M.A., D’Oronzo, E., Facheris, S., Secundo, F., and Savin, S.S., Moscow Univ. Chem. Bull., 2018, vol. 73, no. 1, p. 1. https://doi.org/10.3103/S0027131418020153
Pometun, A.A., Boyko, K.M., Yurchenko, T.S., Nikolaeva, A.Y., Kargov, I.S., Atroshenko, D.L., Savin, S.S., Popov, V.O., and Tishkov, V.I., Biochemistry (Moscow), 2020, vol. 85, no. 6, p. 689. https://doi.org/10.1134/S0006297920060061
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Zidek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S.A.A., Ballard, A.J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., Back, T., Petersen, S., Reiman, D., Clancy, E., Zielinski, M., Steinegger, M., Pacholska, M., Berghammer, T., Bodenstein, S., Silver, D., Vinyals, O., Senior, A.W., Kavukcuoglu, K., Kohli, P., and Hassabis, D., Nature, 2021, vol. 596, no. 7873, p. 583.
Mirdita, M., Schutze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., and Steinegger, M., Nat. Methods, 2022, vol. 19, no. 6, p. 679.
Emsley, P., Lohkamp, B., Scott, W.G., and Cowtan, K., Acta Crystallogr., Sect. D, 2010, vol. 66, no. 4, p. 486.
Alekseeva, A.A., Savin, S.S., Kleimenov, S.Y., Uporov, I.V., Pometun, E.V., and Tishkov, V.I., Biochemistry (Moscow), 2012, vol. 77, no. 10, p. 1199. https://doi.org/10.1134/S0006297912100124
Bradford, M.M., A, Anal. Biochem., 1976, vol. 72, p. 248.
Fogal, S., Beneventi, E., Cendron, L., and Bergantino, E., Appl. Microbiol. Biotechnol., 2015, vol. 99, no. 22, p. 9541.
Sadykhov, E.G., Serov, A.E., Voinova, N.S., Uglanova, S.V., Petrov, A.S., Alekseeva, A.A., Kleimenov, S.Y., Popov, V.O., and Tishkov, V.I., Appl. Biochem. Microbiol., 2006, vol. 42, no. 3, p. 236.
Baker, P.J., Britton, K.L., Rice, D.W., Rob, A., and Stillman, T.J., J. Mol. Biol., 1992, vol. 228, p. 662. https://doi.org/10.1016/0022-2836(92)90848-e
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The research was carried out with partial financial support of the Russian Foundation for Basic Research (project no. 20-04-00915) and partially as a part of state research program.
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Iurchenko, T.S., Loginova, A.A., Sergeev, E.P. et al. Engineering the Active Site of Formate Dehydrogenase from Staphylococcus aureus: Introduction of the Additional Loop and Histigine Residues to the Structure. Moscow Univ. Chem. Bull. 78, 42–53 (2023). https://doi.org/10.3103/S0027131423010078
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DOI: https://doi.org/10.3103/S0027131423010078