3D Structure of D-Аmino Acid Тransaminase from Aminobacterium colombiense in Complex with D-Cycloserine

S. A. Shilova; Шилова С. А.; I. O. Matyuta; Матюта И. О.; E. Yu. Bezsudnova; Безсуднова Е. Ю.; M. E. Minyaev; Миняев М. Е.; A. Yu. Nikolaeva; Николаева А. Ю.; V. O. Popov; Попов В. О.; K. M. Boyko; Бойко К. М.

doi:10.31857/S0023476123600775

3D Structure of D-Аmino Acid Тransaminase from Aminobacterium colombiense in Complex with D-Cycloserine

Authors: Shilova S.A.¹, Matyuta I.O.¹, Bezsudnova E.Y.¹, Minyaev M.E.², Nikolaeva A.Y.¹^,3, Popov V.O.¹, Boyko K.M.⁴
Affiliations:
1. Bach Institute of Biochemistry, Federal Research Center “Fundamentals of Biotechnology,” Russian Academy of Sciences, 119071, Moscow, Russia
2. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
3. National Research Centre “Kurchatov Institute”, 123182, Moscow, Russia
4. 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: 934-940
Section: STRUCTURE OF MACROMOLECULAR COMPOUNDS
URL: https://journals.rcsi.science/0023-4761/article/view/231840
DOI: https://doi.org/10.31857/S0023476123600775
EDN: https://elibrary.ru/HYQYFH
ID: 231840

Cite item

Full Text

Open Access
Restricted Access

Access granted
Restricted Access

Subscription Access

Abstract
About the authors
References
Supplementary files
Statistics

Abstract

D-cycloserine inhibits pyridoxal 5'-phosphate (PLP)-dependent enzymes both reversibly and irreversibly. As an alanine racemase inhibitor, D-cycloserine is used in drug therapy in the treatment of tuberculosis. Several products of the interaction of D-cycloserine and PLP in the active site of the enzyme are known. The crystal structure of the complex of PLP-dependent D-amino acid transaminase from the bacteria Aminobacterium colombiense (Amico) with D-cycloserine obtained at a resolution of 1.9 Å is presented, in which the ring-opened adduct of PLP and D-cycloserine was discovered. In addition, the interaction of D-cycloserine with Amico has been characterized by the kinetic and spectral methods, various products of the interaction of D-cycloserine and PLP in the active site of transaminase have been determined, and the coordination of D-cycloserine and PLP adducts in the Amico active site has been analyzed. It is established that the products of the interaction of D-cycloserine with PLP in the Amico active site are several compounds, including PLP and DCS adducts in the cyclic and open forms, oxime formed by PMP and β-aminooxy-D-alanine, and PMP and β-aminooxypyruvate.

References

Peisach D., Chipman D.M., Van Ophem P.W. et al. // J. Am. Chem. 1998. V. 120. P. 2268. https://doi.org/10.1021/ja973353f
Chiara C. de, Homšak M., Prosser G.A. et al. // Nat. Chem. Biol. 2020. V. 16. P. 686. https://doi.org/10.1038/s41589-020-0498-9
Soper T.S., Manning J.M. // J. Biol. Chem. 1981. V. 256. P. 4263. https://doi.org/10.1016/S0021-9258(19)69428-7
Amorim Franco T.M., Favrot L., Vergnolle O., Blan-chard J.S. // ACS Chem. Biol. 2017. V. 12. P. 1235. https://doi.org/10.1021/acschembio.7b00142
Braunstein A.E. // The Enzymes / Ed. Boyer P.D. London: Academic Press, 1973. P. 379.
Dindo M., Grottelli S., Annunziato G. et al. // Biochem. J. 2019. V. 476. P. 3751. https://doi.org/10.1042/BCJ20190507
Soper T.S., Jones W.M., Lerner B. et al. // J. Biol. Chem. 1977. V. 252. P. 3170. https://doi.org/10.1016/S0021-9258(17)40367-X
Strominger J.L., Ito E., Threnn R.H. // J. Am. Chem. Soc. 1960. V. 82. P. 998. https://doi.org/10.1021/ja01489a058
Walsh C.T. // J. Biol. Chem. 1989. V. 264. P. 2393. https://doi.org/10.1016/S0021-9258(19)81624-1
Caminero J.A., Sotgiu G., Zumla A., Migliori G.B. // Lancet Infect. Dis. 2010. V. 10. P. 621. https://doi.org/10.1016/S1473-3099(10)70139-0
Boyko K., Gorbacheva M., Rakitina T. et al. // Res. Commun. 2014. V. 71. P. 24. https://doi.org/10.1107/S2053230X14025333
Agilent. CrysAlisPRO. Agilent Technologies UK Ltd, 2013.
Vagin A., Teplyakov A. // Acta Cryst. D. 2010. V. 66. P. 22. https://doi.org/10.1107/S0907444909042589
Murshudov G.N., Skubak P., Lebedev A.A. et al. // Acta Cryst. D. 2011. V. 67. P. 355. https://doi.org/10.1107/S0907444911001314
Emsley P., Cowtan K. // Acta Cryst. D. 2004. V. 60. P. 2126. https://doi.org/10.1107/S0907444904019158
Beeler T., Churchich J.E. // J. Biol. Chem. 1976. V. 251. P. 5267. https://doi.org/10.1016/S0021-9258(17)33156-3
Bezsudnova E.Y., Boyko K.M., Nikolaeva A.Y. et al. // Biochimie. 2019. V. 158. P. 130. https://doi.org/10.1016/j.biochi.2018.12.017
Marković-Housley Z., Schimer T., Hohenester E. et al. // Eur. J. Biochem. 1996. V. 236. P. 1025. https://doi.org/10.1111/J.1432-1033.1996.01025.X
Okada K., Hirotsu K., Hayashi H., Kagamiyama H. // Biochemistry. 2001. V. 40. P. 7453. https://doi.org/10.1021/BI010384L
Khomutov A.R., Vepsäläinen J.J., Shvetsov A.S. et al. // Tetrahedron. 1996. V. 52. P. 13751. https://doi.org/10.1016/0040-4020(96)00836-8