Copper ions’ influence on thiocyonate dehydrogenase packing and conformation in a crystal

Capa

Citar

Texto integral

Acesso aberto Acesso aberto
Acesso é fechado Acesso está concedido
Acesso é fechado Acesso é pago ou somente para assinantes

Resumo

The copper-containing enzyme thiocyanate dehydrogenase (TcDH) catalyzes oxidation of thiocyanate to cyanate and elemental sulfur. To date, the spatial structures of two bacterial TcDHs (tpTcDH and pmTcDH) are known. Both enzymes are dimers and contain a trinuclear copper center in the active site. The important difference between these enzymes is that in a crystal, the subunits of the tpTcDH dimer are in identical conformations, while the subunits of the pmTcDH dimer are in different conformations: closed and open. To clarify the role of copper ions in changing the TcDH conformation, the structure of the apo-form of pmTcDH was established, in which both subunits of the dimer had the closed conformation. Soaking of apo-form crystals with copper led to the restoring of the trinuclear center and the conformational rearrangements of the subunits.

Texto integral

Acesso é fechado

Sobre autores

L. Varfolomeeva

Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences

Autor responsável pela correspondência
Email: l.varfolomeeva@fbras.ru
Rússia, Moscow

A. Solovieva

Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences

Email: l.varfolomeeva@fbras.ru
Rússia, Moscow

N. Shipkov

Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences

Email: l.varfolomeeva@fbras.ru
Rússia, Moscow

N. Dergousova

Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences

Email: l.varfolomeeva@fbras.ru
Rússia, Moscow

М. Minyaev

N.D. Zelinsky Institute of Organic Chemistry of the Russian Academy of Sciences

Email: l.varfolomeeva@fbras.ru
Rússia, Moscow

K. Boyko

Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences

Email: l.varfolomeeva@fbras.ru
Rússia, Moscow

T. Tikhonova

Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences

Email: l.varfolomeeva@fbras.ru
Rússia, Moscow

V. Popov

Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences

Email: l.varfolomeeva@fbras.ru
Rússia, Moscow

Bibliografia

  1. Sorokin D.Y., Tourova T.P., Lysenko A.M. et al. // Int. J. Syst. Evol. Microbiol. 2002. V. 52. Pt 2. P. 657. http://dx.doi.org/10.1099/00207713-52-2-657
  2. Slobodkina G.B., Merkel A.Y., Novikov A.A. et al. // Extremophiles. 2020. V. 24. № 1. P. 177. http://dx.doi.org/10.1007/s00792-019-01145-0
  3. Tikhonova T.V., Sorokin D.Y., Hagen W.R. et al. // Proc. Natl. Acad. Sci. USA. 2020. V. 117. № 10. P. 5280. http://dx.doi.org/10.1073/pnas.1922133117
  4. Varfolomeeva L.A., Shipkov N.S., Dergousova N.I. et al. // Int. J. Biol. Macromol. 2024. P. 135058. http://dx.doi.org/10.1016/j.ijbiomac.2024.135058
  5. Varfolomeeva L.A., Solovieva A.Y., Shipkov N.S. et al. // Crystals. 2022. V. 12. P. 1787. http://dx.doi.org/10.3390/cryst12121787
  6. Varfolomeeva L.A., Polyakov K.M., Komolov A.S. et al. // Crystallography Reports. 2023. V. 68. № 6. P. 886. http://dx.doi.org/10.1134/s1063774523600990
  7. McPherson A. // Methods Mol. Biol. 2017. V. 1607. P. 17. http://dx.doi.org/10.1007/978-1-4939-7000-1_2
  8. Atakisi H., Moreau D.W., Thorne R.E. // Acta Cryst. D. 2018. V. 74. № 4. P. 264. http://dx.doi.org/10.1107/S2059798318000207
  9. Kishan K.V., Zeelen J.P., Noble M.E. et al. // Protein Sci. 1994. V. 3. № 5. P. 779. http://dx.doi.org/10.1002/pro.5560030507
  10. Kovari Z., Vas M. // Proteins. 2004. V. 55. № 1. P. 198. http://dx.doi.org/10.1002/prot.10469
  11. Hakansson K., Doherty A.J., Shuman S., Wigley D.B. // Cell. 1997. V. 89. № 4. P. 545. http://dx.doi.org/10.1016/s0092-8674(00)80236-6
  12. Lamzin V.S., Dauter Z., Popov V.O. et al. // J. Mol. Biol. 1994. V. 236. № 3. P. 759. http://dx.doi.org/10.1006/jmbi.1994.1188
  13. Kabsch W. // Acta Cryst. D. 2010. V. 66. № 2. P. 125. http://dx.doi.org/10.1107/S0907444909047337
  14. Agirre J., Atanasova M., Bagdonas H. et al. // Acta Cryst. D. 2023. V. 79. № 6. P. 449. http://dx.doi.org/10.1107/S2059798323003595
  15. Vagin A., Teplyakov A. // Acta Cryst. D. 2010. V. 66. № 1. P. 22. http://dx.doi.org/10.1107/S0907444909042589
  16. Murshudov G.N., Skubak P., Lebedev A.A. et al. // Acta Cryst. D. 2011. V. 67. № 4. P. 355. http://dx.doi.org/10.1107/S0907444911001314
  17. Emsley P., Lohkamp B., Scott W.G., Cowtan K. // Acta Cryst. D. 2010. V. 66. № 4. P. 486. http://dx.doi.org/10.1107/S0907444910007493
  18. Krissinel E., Henrick K. // J. Mol. Biol. 2007. V. 372. № 3. P. 774. http://dx.doi.org/10.1016/j.jmb.2007.05.022
  19. Kabsch W. // Acta Cryst. A. 1976. V. 32. № 5. P. 922. http://dx.doi.org/10.1107/S0567739476001873
  20. Appel M.J., Meier K.K., Lafrance-Vanasse J. et al. // Proc. Natl. Acad. Sci. U S A. 2019. V. 116. № 12. P. 5370. http://dx.doi.org/10.1073/pnas.1818274116
  21. Osipov E.M., Polyakov K.M., Tikhonova T.V. et al. // Acta Cryst. F. 2015. V. 71. № 12. P. 1465. http://dx.doi.org/10.1107/S2053230X1502052X

Arquivos suplementares

Arquivos suplementares
Ação
1. JATS XML
Baixar
2. Fig. 1. Three subunits A, B, C from the independent part of the unit cell (secondary structure is shown) and the symmetrical subunit C (secondary structure is not shown) of the apo form of pmTcDH (PDB ID: 8Z75) (a). The position of the P256 residue in the closed conformation of the subunit of the apo form of pmTcDH (PDB ID: 8Z75) (b) and the open conformation of the holo form of pmTcDH (PDB ID: 8Q9X) (c). The arrow shows the direction of movement of the P256 residue during the opening of the substrate channel. The surface is shown for the amino acid residues forming the walls of the substrate channel. Copper ions of the active site are shown as spheres.

Baixar (504KB)
Metadados
3. Fig. 2. Active center of the apo form of pmTcDH (PDB ID: 8Z75) (a) before infusion of crystals with copper ions. The maximum in the difference electron density map at the 3σ level is described by the copper ion Cu2 with an occupancy of 0.2, the corresponding coordination distances are given in Å (b). Superposition of the structures of the apo form (PDB ID: 8Z75) and holo form (PDB ID: 8Q9X) showed (c) that in the absence of the Cu1 ion, the H346 residue changes its position and forms hydrogen bonds with the E259 residue and a water molecule. Reduction of the trinuclear copper center of pmTcDHCu2+ after infusion of crystals with copper (2+) ions (PDB ID: 8Z76): maxima in the difference electron density map at the 3σ level are shown at the positions of the Cu1, Cu2, Cu3 ions (d). Copper ions and water molecules are large and small spheres, respectively; coordination and hydrogen bonds are thick and thin dotted lines, respectively.

Baixar (529KB)
Metadados
4. Fig. 3. Two positions of the P256 residue on the electron density map (2Fo – Fc), corresponding to the closed and open conformations, in the active site of the C subunit of the pmTcDHCu2+ structure after infusion of crystals with copper ions (2+) (PDB ID: 8Z76) (a). Conformations of the subunits of the pmTcDH dimer after infusion of crystals with copper ions: two closed subunits A and B in the pmTcDHCu2+ structure (PDB ID: 8Z76) (b), open A (top) and closed B (bottom) subunits in the pmTcDHCu+ structure (PDB ID: 8Z77) (c), two open C subunits and a symmetrical C in the pmTcDHCu+ structure (PDB ID: 8Z77) (d). Panels b–d show insets depicting the residues that form the substrate channel.

Baixar (754KB)
Metadados

Declaração de direitos autorais © Russian Academy of Sciences, 2025