- PII
- S0026898425010103-1
- DOI
- 10.31857/S0026898425010103
- Publication type
- Article
- Status
- Published
- Authors
- Volume/ Edition
- Volume 59 / Issue number 1
- Pages
- 141-153
- Abstract
- Thiocyanate dehydrogenase is enzyme catalyzing transformation of a thiocyanate ion into a cyanate ion with outcome of two electrons, two protons and a neutral atom of sulphur. Earlier structures of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus were solved. Despite not perfect quality of the structures (twinning and pronounced anisotropy of the crystals, incomplete occupancy of the copper ions, absence of data for complexes with analogues of the substrate), there was suggested a mechanism of the enzyme functioning based on those structures. Recently at atomic resolution there have been solved structures of a gene-modified copy of relative enzyme from Pelomicrobium methylotrophicum for free protein and its complex with thiourea. In the new structures copper ions of the active site possess complete occupancy. In these structures it is possible to reliably identify two conformations of the protein molecule with opened and closed active sites. The new structural high resolution data also allowed us to determine the presence of the superposition of different states of the copper ions for each of the two conformations. In each state the copper ions have different oxidation degrees, different corresponding ligands and partial occupancies. The ion charges were determined according to the ions coordination. In the protein molecule with the closed active site the complexes with inhibitor (thiourea ion) and molecular oxygen are observed. The complex with thiourea allows us to model binding of thiocyanate ion to the enzyme molecule. Taking into account the changes of the structures in the opened and closed conformations, a mechanism of the attacking oxygen ligand activation is suggested. A new scheme of the enzymatic reaction is discussed.
- Keywords
- рентгеноструктурный анализ белков конформационные изменения медьсодержащие ферменты ферментативные реакции
- Date of publication
- 14.09.2025
- Year of publication
- 2025
- Number of purchasers
- 0
- Views
- 6
References
- 1. Tikhonova T.V., Sorokin D.Y., Hagen W.R., Khrenova M.G., Muyzer G., Rakitina T.V., Shabalin I.G., Trofimov A.A., Tsallagov S.I., Popov V.O. (2020) Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase. Proc. Natl. Acad. Sci. USA. 117, 5280‒5290. https://doi.org/10.1073/pnas.1922133117
- 2. Varfolomeeva L.A., Polyakov K.M., Komolov A.S., Rakitina T.V., Dergousova N.I., Dorovatovskii P.V., Boyko K.M., Tikhonova T.V., Popov V.O. (2023) Improvement of the diffraction properties of thiocyanate dehydrogenase crystals. Crystallography Repts. 68, 886−891. https://doi.org/10.1134/s1063774523600990
- 3. Haltia T., Brown K., Tegoni M., Cambillau C., Saraste M., Mattila K., Djinovic-Carugo K. (2003) Crystal structure of nitrous oxide reductase from Paracoccus denitrificans at 1.6 Å resolution. Biochem. J. 369, 77−88. https://doi.org/10.1042/BJ20020782
- 4. Krissinel E., Henrick K. (2007) Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774−797. https://doi.org/10.1016/j.jmb.2007.05.022
- 5. Solomon E.I., Heppner D.E., Johnston E.M., Ginsbach J.W., Cirera J., Qayyum M., Kieber-Emmons M.T., Kjaergaard C.H., Hadt R.G., Tian L. (2014) Copper active sites in biology. Chem. Rev. 114, 3659−3853. https://doi.org/10.1021/cr400327t
- 6. Rubino J.T., Frank K.J. (2012) Coordination chemistry of copper proteins: how nature handles a toxic cargo for essential function. J. Inorg. Biochem. 107, 129‒143. https://doi.org/10.1016/j.jinorgbio.2011.11.024
- 7. Cotton F.A., Wilkinson G. (1980) Advanced Inorganic Chemistry, 4th ed. New York: John Wiley and Sons, 798–821.
- 8. Balamurugan R., Palaniandavar M., Gopalan R.S. (2001) Trigonal planar copper(I) complex: synthesis, structure, and spectra of a redox pair of novel copper(II/I) complexes of tridentate bis(benzimidazol-2’-vl) ligand framework as models for electron-transfer copper proteins. Inorg. Chem. 40, 2246–2255. https://doi.org/10.1021/ic0003372
- 9. Reinen D., Friebel C. (1984) Copper(2+) in 5-coordination: a case of a second-order Jahn-Teller effect. 2. Pentachlorocuprate(3-) and other CuIIL5 complexes: trigonal bipyramid or square pyramid? Inorg. Chem. 23, 791–798. https://doi.org/10.1021/ic00175a001
- 10. Wansapura C.M., Juyong C., Simpson J.L., Szymanski D., Eaton G.R., Eaton S.S., Fox S. (2003) From planar toward tetrahedral copper(Il) complexes: structural and electron paramagnetic resonance studies of substituent steric effects in an extended class of pyrrolate-imine ligands. J. Coord. Chem. 56, 975–993. https://doi.org/10.1080/00958970310001607752
- 11. Hatfield W.E. (1997) Handbook of Copper Compounds and Applications. Ed. Richardson H.W. New York: Marcel Dekker, 13–30.
- 12. Raithby P.R., Shields G.P., Allen F.H., Motherwell W.D.S. (2000) Structure correlation study of four-coordinate copper(I) and (II) complexes. Acta Cryst. B56, 444–454. https://doi.org/10.1107/S0108768199016870
- 13. Komori H., Sugiyama R., Kataoka K., Miyazaki K., Higuchi Y., Sakurai T. (2014) New insights into the catalytic active-site structure of multicopper oxidases. Acta Cryst. D70, 772–779. https://doi.org/10.1107/S1399004713033051
- 14. Polyakov K.M., Gavryushov S., Ivanova S., Fedorova T.V., Glazunova O.A., Popov A.N., Koroleva O.V. (2017) Structural study of the X-ray-induced enzymatic reduction of molecular oxygen to water by Steccherinum murashkinskyi laccase: insights into the reaction mechanism. Acta Cryst. D73, 388–401. https://doi.org/10.1107/S2059798317003667
- 15. Derewenda Z.S. (2010) Application of protein engineering to enhance crystallizability and improve crystal properties. Acta Cryst. D66, 604–615. doi: 10.1107/S090744491000644X.
- 16. Vagin A., Teplyakov A. (1997) MOLREP: An automated program for molecular replacement. J. Appl. Сryst. 66, 22–25. https://doi.org/10.1107/S0021889897006766
- 17. Murshudov G.N., Vagin A.A., Dodson E.J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Cryst. D53, 240–255. https://doi.org/10.1107/S0907444996012255
- 18. McNicholas S., Potterton E., Wilson K.S., Noble M.E.M. (2011) Presenting your structures: the CCP4mg molecular-graphics software. Acta Cryst. D67, 386–394. https://doi.org/10.1107/S0907444910045749
