Improvement of the Diffraction Properties of Thiocyanate Dehydrogenase Crystals

L. A. Varfolomeeva; Варфоломеева Л. А.; K. M. Polyakov; Поляков К. М.; A. S. Komolov; Комолов А. С.; T. V.  Rakitina; Ракитина Т. В.; N. I. Dergousova; Дергоусова Н. И.; P. V. Dorovatovskii; Дороватовский П. В.; K. M. Boyko; Бойко К. М.; T. V. Tikhonova; Тихонова Т. В.; V. O. Popov; Попов В. О.

doi:10.31857/S0023476123600799

Improvement of the Diffraction Properties of Thiocyanate Dehydrogenase Crystals

Authors: Varfolomeeva L.A.¹, Polyakov K.M.², Komolov A.S.³, Rakitina T.V.³^,4, Dergousova N.I.¹, Dorovatovskii P.V.³, Boyko K.M.⁵, Tikhonova T.V.¹, Popov V.O.¹
Affiliations:
1. Federal Research Center “Fundamentals of Biotechnology,” Russian Academy of Sciences, 119071, Moscow, Russia
2. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia
3. National Research Centre “Kurchatov Institute”, 123182, Moscow, Russia
4. Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
5. Bach Institute of Biochemistry, Federal Research Center “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 117071, Moscow, Russia
Issue: Vol 68, No 6 (2023)
Pages: 888-893
Section: STRUCTURE OF MACROMOLECULAR COMPOUNDS
URL: https://journals.rcsi.science/0023-4761/article/view/231817
DOI: https://doi.org/10.31857/S0023476123600799
EDN: https://elibrary.ru/ABAVXD
ID: 231817

Cite item

Full Text

Abstract
About the authors
References
Supplementary files
Statistics

Abstract

During determination of the thiocyanate dehydrogenase (TcDH) structure difficulties have occurred, related to the fact that enzyme crystals have been either twinned or strongly anisotropic. The diffraction quality of crystals can be improved by using mutant forms as objects of a study or by studying the structure of a related enzyme from another organism. Based on the analysis of the oligomeric structure of TcDH, the mutant forms of the enzyme that are promising for improving the diffraction properties have been proposed. The crystals have been obtained and the structures of the TcDH mutant forms with the substitutions T169A and K281A have been solved. The structure of the mutant form with the substitution T169A is found to be similar to the previously solved structures. In the structure of the mutant form with the substitution K281A, a change in the tetramer structure that made twinning impossible has been detected.

References

Sorokin D.Y., Tourova T.P., Lysenko A.M. et al. // Int. J. Syst. Evol. Microbiol. 2002. V. 52. P. 657. https://doi.org/10.1099/00207713-52-2-657
Tikhonova T.V., Sorokin D.Y., Hagen W.R. et al // Proc. Natl. Acad. Sci. USA. 2020. V. 117. P. 5280. https://doi.org/10.1073/pnas.1922133117
Paraskevopoulos K., Antonyuk S.V., Sawers R.G. et al. // J. Mol. Biol. 2006. V. 362. P. 55. https://doi.org/10.1016/j.jmb.2006.06.064
Lebedev A.A., Vagin A.A., Murshudov G.N. // Acta Cryst. D. 2006. V. 62. P. 83. https://doi.org/10.1107/S0907444905036759
Murshudov G.N., Skubák P., Lebedev A.A. et al. // Acta Cryst. D. 2011. V. 67. P. 355. https://doi.org/10.1107/S0907444911001314
Campeotto I., Lebedev A., Schreurs A.M.M. et al. // Sci. Rep. 2018. V. 8. P. 14876. https://doi.org/10.1038/s41598-018-32962-6
Yeates T.O. // Methods Enzymol. 1997. V. 276. P. 344. https://doi.org/10.1016/S0076-6879(97)76068-3
Padilla J.E., Yeates T.O. // Acta Cryst. D. 2003. V. 59. P. 1124. https://doi.org/10.1107/S0907444903007947
Yang F., Dauter Z., Wlodawer A. // Acta Cryst. D. 2000. V. 56. P. 959. https://doi.org/10.1107/S0907444900007162
Derewenda Z. S. // Acta Cryst. D. 2010. V. 66. P. 604. https://doi.org/10.1107/S090744491000644X
Longenecker K.L., Garrard S.M., Sheffield P.J., Derewenda Z.S. // Acta Cryst. D. 2001. V. 57. P. 679. https://doi.org/10.1107/S0907444901003122
Malawski G.A., Hillig R.C., Monteclaro F. et al. // Protein Sci. 2006. V. 15. P. 2718. https://doi.org/10.1110/ps.062491906
Neau D.B., Gilbert N.C., Bartlett S.G. et al. // Acta Cryst. F. 2007. V. 63. P. 972. https://doi.org/10.1107/S1744309107050993
Backmark A., Nyblom M., Törnroth-Horsefield S. et al. // Acta Cryst. D. 2008. V. 64. P. 1183. https://doi.org/10.1107/S090744490802948X
Svetogorov R.D., Dorovatovskii P.V., Lazarenko V.A. // Cryst. Res. Technol. 2020. V. 55. P. 1900184. https://doi.org/1002/crat.201900184
Kabsch W. // Acta Cryst. D. 2010. V. 66. P. 125. https://doi.org/10.1107/S0907444909047337
Vagin A., Teplyakov A. // Acta Cryst. D. 2010. V. 66. P. 22. https://doi.org/10.1107/S0907444909042589
Winn M.D., Ballard C.C., Cowtan K.D. et al. // Acta Cryst. D. 2011. V. 67. P. 235. https://doi.org/10.1107/S0907444910045749
Emsley P., Lohkamp B., Scott W.G., Cowtan K. // Acta Cryst. D. 2010. V. 66. P. 486. https://doi.org/10.1107/S0907444910007493
Krissinel E., Henrick K. // J. Mol. Biol. 2007. V. 372. P. 774. https://doi.org/10.1016/j.jmb.2007.05.022