Mechanism of D-cycloserine inhibition of D-amino acid transaminase from Haliscomenobacter hydrossis

Cover Page

Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription Access

Abstract

D-cycloserine inhibits pyridoxal-5′-phosphate (PLP)-dependent enzymes. The inhibition efficiency depends on the organization of their active center and the mechanism of the catalyzed reaction. D-cycloserine interacts with the PLP form of enzyme similarly to substrate amino donor, and the interaction is predominantly reversible. Inhibition products include hydroxyisoxazole-pyridoxamine-5′-phosphate, oxime between PLP and β-aminooxy-D-alanine, ketimine between pyridoxamine-5′-phosphate and cyclic or open forms of D-cycloserine, pyridoxamine-5′-phosphate, etc. For some enzymes the formation of a stable aromatic product - hydroxyisoxazole can lead to irreversible D-cycloserine inhibition at certain pH value. The aim of this work was to study the mechanism of D-cycloserine inhibition of PLP-dependent D-amino acid transaminase from the bacterium Haliscomenobacter hydrossis. Spectral methods revealed several products of the interaction of D-cycloserine with PLP in the active site of transaminase: oxime between PLP and β-aminooxy-D-alanine, ketimine between pyridoxamine-5′-phosphate and cyclic or open forms of D-cycloserine, pyridoxamine-5′-phosphate. The formation of hydroxyisoxazole-pyridoxamine-5′-phosphate was not observed. The 3D structure of the complex of transaminase with D-cycloserine was obtained by X-ray diffraction analysis. In the active site of transaminase, a ketimine adduct between pyridoxamine-5′-phosphate and D-cycloserine in the cyclic form was found; the ketimine occupied two positions and was coordinated via hydrogen bonds with different active site residues. Using kinetic and spectral methods we have shown that D-cycloserine inhibition is reversible, and the activity of transaminase from H. hydrossis can be restored by adding an excess of keto substrate as well as by adding an excess of cofactor. The results obtained confirm the reversibility of D-cycloserine inhibition and the conversion of various adducts of D-cycloserine and PLP into each other.

About the authors

A. K Bakunova

Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences

Email: a.bakunova@fbras.ru
119071 Moscow, Russia

I. O Matyuta

Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences

Email: a.bakunova@fbras.ru
119071 Moscow, Russia

A. Yu Nikolaeva

Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences;Kurchatov Complex of NBICS-Technologies, National Research Centre “Kurchatov Institute”

Email: a.bakunova@fbras.ru
119071 Moscow, Russia;123182 Moscow, Russia

K. M Boyko

Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences

Email: a.bakunova@fbras.ru
119071 Moscow, Russia

V. O Popov

Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences;Faculty of Biology, Lomonosov Moscow State University

Email: a.bakunova@fbras.ru
119071 Moscow, Russia;119991 Moscow, Russia

E. Yu Bezsudnova

Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences

Email: eubez@inbi.ras.ru
119071 Moscow, Russia

References

  1. Peisach, D., Chipman, D. M., Van Ophem, P. W., Manning, J. M., and Ringe, D. (1998) D-Cycloserine inactivation of D-amino acid aminotransferase leads to a stable noncovalent protein complex with an aromatic cycloserine-PLP derivative, J. Am. Chem. Soc., 120, 2268-2274, doi: 10.1021/ja973353f.
  2. Fenn, T. D., Stamper, G. F., Morollo, A. A., and Ringe, D. (2003) A side reaction of alanine racemase: transamination of cycloserine, Biochemistry, 42, 5775-5783, doi: 10.1021/bi02702 2d.
  3. Amorim Franco, T. M., Favrot, L., Vergnolle, O., and Blanchard, J. S. (2017) Mechanism-based inhibition of the Mycobacterium tuberculosis branched-chain aminotransferase by d- and l-cycloserine, ACS Chem. Biol., 12, 1235-1244, doi: 10.1021/acschembio.7b00142.
  4. Dindo, M., Grottelli, S., Annunziato, G., Giardina, G., Pieroni, M., Pampalone, G., Faccini, A., Cutruzzolà, F., Laurino, P., Costantino, G., and Cellini, B. (2019) Cycloserine enantiomers are reversible inhibitors of human alanine:glyoxylate aminotransferase: implications for Primary Hyperoxaluria type 1, Biochem. J., 476, 3751-3768, doi: 10.1042/BCJ20190507.
  5. Malashkevich, V. N., Strop, P., Keller, J. W., Jansonius, J. N., and Toney, M. D. (1999) Crystal structures of dialkylglycine decarboxylase inhibitor complexes, J. Mol. Biol., 294, 193-200, doi: 10.1006/jmbi.1999.3254.
  6. Caminero, J. A., Sotgiu, G., Zumla, A., and Migliori, G. B. (2010) Best drug treatment for multidrug-resistant and extensively drug-resistant tuberculosis, Lancet. Infect. Dis., 10, 621-629, doi: 10.1016/S1473-3099(10)70139-0.
  7. De Chiara, C., Homšak, M., Prosser, G. A., Douglas, H. L., Garza-Garcia, A., Kelly, G., Purkiss, A. G., Tate, E. W., and de Carvalho, L. P. S. (2020) D-Cycloserine destruction by alanine racemase and the limit of irreversible inhibition, Nat. Chem. Biol., 16, 686-694, doi: 10.1038/s41589-020-0498-9.
  8. Priyadarshi, A., Lee, E. H., Sung, M. W., Nam, K. H., Lee, W. H., Kim, E. E., and Hwang, K. Y. (2009) Structural insights into the alanine racemase from Enterococcus faecalis, Biochim. Biophys. Acta, 1794, 1030-1040, doi: 10.1016/j.bbapap.2009.03.006.
  9. Noda, M., Matoba, Y., Kumagai, T., and Sugiyama, M. (2004) Structural evidence that alanine racemase from a D-cycloserine-producing microorganism exhibits resistance to its own product, J. Biol. Chem., 279, 46153-46161, doi: 10.1074/jbc.M404605200.
  10. Wu, D., Hu, T., Zhang, L., Chen, J., Du, J., Ding, J., Jiang, H., and Shen, X. (2008) Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: enzymatic characterization with crystal structure analysis, Protein Sci., 17, 1066-1076, doi: 10.1110/ps.083495908.
  11. Tassoni, R., van der Aart, L. T., Ubbink, M., van Wezel, G. P., and Pannu, N. S. (2017) Structural and functional characterization of the alanine racemase from Streptomyces coelicolor A3(2), Biochem. Biophys. Res. Commun., 483, 122-128, doi: 10.1016/j.bbrc.2016.12.183.
  12. Duff, S. M. G., Rydel, T. J., McClerren, A. L., Zhang, W., Li, J. Y., Sturman, E. J., Halls, C., Chen, S., Zeng, J., Peng, J., Kretzler, C. N., and Evdokimov, A. (2012) The enzymology of alanine aminotransferase (AlaAT) isoforms from Hordeum vulgare and other organisms, and the HvAlaAT crystal structure, Arch. Biochem. Biophys., 528, 90-101, doi: 10.1016/j.abb.2012.06.006.
  13. Bharath, S. R., Bisht, S., Harijan, R. K., Savithri, H. S., and Murthy, M. R. N. (2012) Structural and mutational studies on substrate specificity and catalysis of Salmonella typhimurium D-cysteine desulfhydrase, PLoS One, 7, e36267, doi: 10.1371/journal.pone.0036267.
  14. Braunstein, A. E. (1973) Amino group transfer, The enzymes, (Boyer, P., ed.) Academic Press, N.Y., pp. 379-481, doi: 10.1016/S1874-6047(08)60122-5.
  15. Eliot, A. C., and Kirsch, J. F. (2004) Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations, Annu. Rev. Biochem., 73, 383-415, doi: 10.1146/annurev.biochem.73.011303.074021.
  16. Toney, M. D. (2011) Controlling reaction specificity in pyridoxal phosphate enzymes, Biochim. Biophys. Acta., 1814, 1407-1418, doi: 10.1016/j.bbapap.2011.05.019.
  17. Soper, T. S., and Manning, J. M. (1981) Different modes of action of inhibitors of bacterial D-amino acid transaminase. A target enzyme for the design of new antibacterial agents, J. Biol. Chem., 256, 4263-4268, doi: 10.1016/s0021-9258(19)69428-7.
  18. Bakunova, A. K., Nikolaeva, A. Y., Rakitina, T. V., Isaikina, T. Y., Khrenova, M. G., Boyko, K. M., Popov, V. O., and Bezsudnova, E. Y. (2021) The uncommon active site of D-amino acid transaminase from Haliscomenobacter hydrossis: biochemical and structural insights into the new enzyme, Molecules, 26, 5053, doi: 10.3390/molecules26165053.
  19. Morrison, J. F., and Walsh, C. T. (1998) The behavior and significance of slow-binding enzyme inhibitors, Adv. Enzymol. Relat. Areas Mol. Biol., 61, 201-301, doi: 10.1002/9780470123072.ch5.
  20. Winter, G., Waterman, D. G., Parkhurst, J. M., Brewster, A. S., Gildea, R. J., Gerstel, M., Fuentes-Montero, L., Vollmar, M., Michels-Clark, T., Young, I. D., Sauter, N. K., and Evans, G. (2018) DIALS: implementation and evaluation of a new integration package, Acta Crystallogr. Sect. D Struct. Biol., 74, 85-97, doi: 10.1107/S2059798317017235.
  21. Collaborative Computational Project, N. 4 (1994) The CCP4 suite: programs for protein crystallography, Acta Crystallogr. Sect. D Biol. Crystallogr., 50, 760-763, doi: 10.1107/S0907444994003112.
  22. Vagin, A., and Teplyakov, A. (1997) MOLREP: an automated program for molecular replacement, J. Appl. Crystallogr., 30, 1022-1025, doi: 10.1107/S0021889897006766.
  23. Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F., and Vagin, A. A. (2011) REFMAC 5 for the refinement of macromolecular crystal structures, Acta Crystallogr. Sect. D Biol. Crystallogr., 67, 355-367, doi: 10.1107/S0907444911001314.
  24. Emsley, P., and Cowtan, K. (2004) Coot: model-building tools for molecular graphics, Acta Crystallogr. Sect. D Biol. Crystallogr., 60, 2126-2132, doi: 10.1107/S0907444904019158.
  25. Krissinel, E., and Henrick, K. (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions, Acta Crystallogr. Sect. D Biol. Crystallogr., 60, 2256-2268, doi: 10.1107/S0907444904026460.
  26. Beeler, T., and Churchich, J. E. (1976) Reactivity of the phosphopyridoxal groups of cystathionase, J. Biol. Chem., 251, 5267-5271, doi: 10.1016/S0021-9258(17)33156-3.
  27. Honikel, K. O., and Madsen, N. B. (1972) Comparison of the absorbance spectra and fluorescence behavior of phosphorylase b with that of model pyridoxal phosphate derivatives in various solvents, J. Biol. Chem., 247, 1057-1064, doi: 10.1016/S0021-9258(19)45615-9.
  28. Delbaere, L. T. J., Kallen, J., Markovic-Housley, Z., Khomutov, A. R., Khomutov, R. M., Karpeisky, M. Y., and Jansonius, J. N. (1989) Complexes of aspartate aminotransferase with hydroxylamine derivatives: spectral studies in solution and in the crystalline state, Biochimie, 71, 449-459, doi: 10.1016/0300-9084(89)90175-2.
  29. Okada, K., Hirotsu, K., Hayashi, H., and Kagamiyama, H. (2001) Structures of Escherichia coli branched-chain amino acid aminotransferase and its complexes with 4-methylvalerate and 2-methylleucine: induced fit and substrate recognition of the enzyme, Biochemistry, 40, 7453-7463, doi: 10.1021/bi010384l.
  30. Peisach, D., Chipman, D. M., Van Ophem, P. W., Manning, J. M., and Ringe, D. (1998) Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase, Biochemistry, 37, 4958-4967, doi: 10.1021/bi972884d.
  31. Marković-Housley, Z., Schirmer, T., Hohenester, E., Khomutov, A. R., Khomutov, R. M., Karpeisky, M. Y., Sandmeier, E., Christen, P., and Jansonius, J. N. (1996) Crystal structures and solution studies of oxime adducts of mitochondrial aspartate aminotransferase, Eur. J. Biochem., 236, 1025-1032, doi: 10.1111/j.1432-1033.1996.01025.x.
  32. Di Salvo, M. L., Contestabile, R., and Safo, M. K. (2011) Vitamin B(6) salvage enzymes: mechanism, structure and regulation, Biochim. Biophys. Acta, 1814, 1597-1608, doi: 10.1016/j.bbapap.2010.12.006.
  33. Thirstrup, K., Christensen, S., Møller, H. A., Ritzén, A., Bergström, A. L., Sager, T. N., and Jensen, H. S. (2011) Endogenous 2-oxoglutarate levels impact potencies of competitive HIF prolyl hydroxylase inhibitors, Pharmacol. Res., 64, 268-273, doi: 10.1016/j.phrs.2011.03.017.

Copyright (c) 2023 Russian Academy of Sciences

This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies