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Abstract:

Dissimilatory nitrite reductases are key enzymes in the denitrification pathway, reducing nitrite and leading to the production of gaseous products (NO, N2O and N2). The reaction is catalysed either by a Cu-containing nitrite reductase (NirK) or by a cytochrome cd 1 nitrite reductase (NirS), as the simultaneous presence of the two enzymes has never been detected in the same microorganism. The thermophilic bacterium Thermus scotoductus SA-01 is an exception to this rule, harbouring both genes within a denitrification cluster, which encodes for an atypical NirK. The crystal structure of TsNirK has been determined at 1.63Å resolution. TsNirK is a homotrimer with subunits of 451 residues that contain three copper atoms each. The N-Terminal region possesses a type 2 Cu (T2Cu) and a type 1 Cu (T1CuN) while the C-Terminus contains an extra type 1 Cu (T1CuC) bound within a cupredoxin motif. T1CuN shows an unusual Cu atom coordination (His2-Cys-Gln) compared with T1Cu observed in NirKs reported so far (His2-Cys-Met). T1CuC is buried at ∼5Å from the molecular surface and located ∼14.1Å away from T1CuN; T1CuN and T2Cu are ∼12.6Å apart. All these distances are compatible with an electron-Transfer process T1CuC → T1CuN → T2Cu. T1CuN and T2Cu are connected by a typical Cys-His bridge and an unexpected sensing loop which harbours a SerCAT residue close to T2Cu, suggesting an alternative nitrite-reduction mechanism in these enzymes. Biophysicochemical and functional features of TsNirK are discussed on the basis of X-ray crystallography, electron paramagnetic resonance, resonance Raman and kinetic experiments. © 2019.

Registro:

Documento: Artículo
Título:A three-domain copper-nitrite reductase with a unique sensing loop
Autor:Opperman, D.J.; Murgida, D.H.; Dalosto, S.D.; Brondino, C.D.; Ferroni, F.M.
Filiación:Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, Free State, 9300, South Africa
Departamento de Química Inorgánica, Analítica y Química Física and INQUIMAE (CONICET-UBA), Universidad de Buenos Aires, Pab. 2 piso 1, Buenos Aires, Buenos Aires, C1428EHA, Argentina
Instituto de Física Del Litoral, CONICET-UNL, Güemes 3450, Santa Fe, Santa Fe, S3000ZAA, Argentina
Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional Del Litoral (UNL), Paraje El Pozo, Santa Fe, Santa Fe, S3000ZAA, Argentina
Palabras clave:Ser; Thermus scotoductus SA-01; three-domain copper-nitrite reductase; X-ray crystal structure
Año:2019
Volumen:6
Página de inicio:248
Página de fin:258
DOI: http://dx.doi.org/10.1107/S2052252519000241
Título revista:IUCrJ
Título revista abreviado:IUCrJ
ISSN:20522525
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_20522525_v6_n_p248_Opperman

Referencias:

  • Abraham, Z.H.L., Lowe, D.J., Smith, B.E., (1993) Biochem. J, 295, pp. 587-593
  • Adman, E.T., Godden, J.W., Turley, S., (1995) J. Biol. Chem, 270, pp. 27458-27474
  • Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J., (1990) J. Mol. Biol, (215), pp. 403-410
  • Andrew, C.R., Yeom, H., Valentine, J.S., Karlsson, B.G., Van Pouderoyen, G., Canters, G.W., Loehr, T.M., Bonander, N., (1994) J. Am. Chem. Soc, 116, pp. 11489-11498
  • Antonyuk, S.V., Han, C., Eady, R.R., Hasnain, S.S., (2013) Nature, 496, pp. 123-126
  • Borgonie, G., García-Moyano, A., Litthauer, D., Bert, W., Bester, A., Van Heerden, E., Möller, C., Onstott, T.C., (2011) Nature, (474), pp. 79-82
  • Boulanger, M.J., Murphy, M.E.P., (2009) Protein Sci, 12, pp. 248-256
  • Boulanger, M.J., Kukimoto, M., Nishiyama, M., Horinouchi, S., Murphy, M.E.P., (2000) J. Biol. Chem, 275, pp. 23957-23964
  • Boulanger, M.J., Murphy, M.E.P., (2001) Biochemistry, 40, pp. 9132-9141
  • Boulanger, M.J., Murphy, M.E.P., (2002) J. Mol. Biol, 315, pp. 1111-1127
  • Bradford, M.M., (1976) Anal Biochem, 72, pp. 248-254
  • Brenner, S., Heyes, D.J., Hay, S., Hough, M.A., Eady, R.R., Hasnain, S.S., Scrutton, N.S., (2009) J. Biol. Chem, 284, pp. 25973-25983
  • Bueno, E., Bedmar, E.J., Richardson, D.J., Delgado, M.J., (2008) FEMS Microbiol. Lett, 279, pp. 188-194
  • Buning, C., Canters, G.W., Comba, P., Dennison, C., Jeuken, L., Melter, M., Sanders-Loehr, J., (2000) J. Am. Chem. Soc, 122, pp. 204-211
  • Chai, J.-D., Head-Gordon, M., (2008) Phys. Chem. Chem. Phys, 10, pp. 6615-6620
  • Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M., Ferguson, D.M., Spellmeyer, D.C., Kollman, P.A., (1995) J. Am. Chem. Soc, 117, pp. 5179-5197
  • Cristaldi, J.C., Gómez, M.C., González, P.J., Ferroni, F.M., Dalosto, S.D., Rizzi, A.C., Rivas, M.G., Brondino, C.D., (2018) Biochim. Biophys. Acta, (1862), pp. 752-760
  • Debeer George, S., Basumallick, L., Szilagyi, R.K., Randall, D.W., Hill, M.G., Nersissian, A.M., Valentine, J.S., Solomon, E.I., (2003) J. Am. Chem. Soc, 125, pp. 11314-11328
  • Dundas, J., Ouyang, Z., Tseng, J., Binkowski, A., Turpaz, Y., Liang, J., (2006) Nucleic Acids Res, 34, pp. W116-W118
  • Ellis, M.J., Grossmann, J.G., Eady, R.R., Hasnain, S.S., (2007) J. Biol. Inorg. Chem, 12, pp. 1119-1127
  • Emsley, P., Lohkamp, B., Scott, W.G., Cowtan, K., (2010) Acta Cryst D, 66, pp. 486-501
  • Evans, P., (2006) Acta Cryst D, 62, pp. 72-82
  • Evans, P.R., Murshudov, G.N., (2013) Acta Cryst D, 69, pp. 1204-1214
  • Felsenstein, J., (1985) Evolution, 39, pp. 783-791
  • Ferroni, F.M., Guerrero, S.A., Rizzi, A.C., Brondino, C.D., (2012) J. Inorg. Biochem, 114, pp. 8-14
  • Ferroni, F.M., Marangon, J., Neuman, N.I., Cristaldi, J.C., Brambilla, S.M., Guerrero, S.A., Rivas, M.G., Brondino, C.D., (2014) J. Biol. Inorg. Chem, (19), pp. 913-921
  • Fowler, D., Coyle, M., Skiba, U., Sutton, M.A., Cape, J.N., Reis, S., Sheppard, L.J., Voss, M., (2014) Philos. Trans. R. Soc. B Biol. Sci, 368, p. 20130164
  • Fukuda, Y., Koteishi, H., Yoneda, R., Tamada, T., Takami, H., Inoue, T., Nojiri, M., (2014) Biochim. Biophys. Acta, 1837, pp. 396-405
  • Fukuda, Y., Tse, K.M., Lintuluoto, M., Fukunishi, Y., Mizohata, E., Matsumura, H., Takami, H., Inoue, T., (2014) J. Biochem, 155, pp. 123-135
  • Fukuda, Y., Tse, K.M., Suzuki, M., Diederichs, K., Hirata, K., Nakane, T., Sugahara, M., Mizohata, E., (2016) J. Biochem, 159, pp. 527-538
  • Gounder, K., Brzuszkiewicz, E., Liesegang, H., Wollherr, A., Daniel, R., Gottschalk, G., Reva, O., Litthauer, D., (2011) BMC Genomics, (12), pp. 577-577
  • Gruber, N., Galloway, J.N., (2008) Nature, 451, pp. 293-296
  • Han, C., Wright, G.S., Fisher, K., Rigby, S.E., Eady, R.R., Hasnain, S.S., (2012) Biochem. J, 444, pp. 219-226
  • Han, J., Adman, E.T., Beppu, T., Codd, R., Freeman, H.C., Huq, L., Loehr, T.M., Sanders-Loehr, J., (1991) Biochemistry, 30, pp. 10904-10913
  • Han, J., Loehr, T.M., Lu, Y., Valentine, J.S., Averill, B.A., Sanders-Loehr, J., (1993) J. Am. Chem. Soc, 115, pp. 4256-4263
  • Holm, R.H., Kennepohl, P., Solomon, E.I., (1996) Chem. Rev, (96), pp. 2239-2314
  • Horrell, S., Kekilli, D., Strange, R.W., Hough, M.A., (2017) Metallomics, (9), pp. 1470-1482
  • Hough, M.A., Eady, R.R., Hasnain, S.S., (2008) Biochemistry, 47, pp. 13547-13553
  • Hough, M.A., Ellis, M.J., Antonyuk, S., Strange, R.W., Sawers, G., Eady, R.R., Hasnain, S.S., (2005) J. Mol. Biol, 350, pp. 300-309
  • Kabsch, W., (2010) Acta Cryst D, 66, pp. 125-132
  • Kataoka, K., Furusawa, H., Takagi, K., Yamaguchi, K., Suzuki, S., (2000) J. Biochem, 127, pp. 345-350
  • Kataoka, K., Yamaguchi, K., Sakai, S., Takagi, K., Suzuki, S., (2003) Biochem. Biophys. Res. Commun, 303, pp. 519-524
  • Klotz, I.M., Klotz, T.A., (1955) Science, 121, pp. 477-480
  • Kumar, S., Stecher, G., Tamura, K., (2016) Mol. Biol. Evol, 33, pp. 1870-1874
  • Laemmli, U.K., Beguin, F., Gujer-Kellenberger, G., (1970) J. Mol. Biol, 47, pp. 69-85
  • Leferink, N.G.H., Han, C., Antonyuk, S.V., Heyes, D.J., Rigby, S.E.J., Hough, M.A., Eady, R.R., Hasnain, S.S., (2011) Biochemistry, 50, pp. 4121-4131
  • Lipman, D.J., Pearson, W.R., (1985) Science, 227, pp. 1435-1441
  • Magnabosco, C., Tekere, M., Lau, M.C.Y., Linage, B., Kuloyo, O., Erasmus, M., Cason, E., Onstott, T.C., (2014) Front. Microbiol, (5), p. 679
  • McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C., Read, R.J., (2007) J. Appl. Cryst, 40, pp. 658-674
  • Merkle, A.C., Lehnert, N., (2009) Inorg. Chem, 48, pp. 11504-11506
  • Merkle, A.C., Lehnert, N., (2012) Dalton Trans, 41, pp. 3355-3368
  • Murshudov, G.N., Skubák, P., Lebedev, A.A., Pannu, N.S., Steiner, R.A., Nicholls, R.A., Winn, M.D., Vagin, A.A., (2011) Acta Cryst D, 67, pp. 355-367
  • Murugapiran, S.K., Huntemann, M., Wei, C.-L., Han, J., Detter, J.C., Han, C., Erkkila, T.H., Hedlund, B.P., (2013) Stand. Genomic Sci, 7, pp. 449-468
  • Nersissian, A.M., Mehrabian, Z.B., Nalbandyan, R.M., Hart, P.J., Fraczkiewicz, G., Czernuszewicz, R.S., Bender, C.J., Valentine, J.S., (1996) Protein Sci, 5, pp. 2184-2192
  • Nestor, L., Larrabee, J.A., Woolery, G., Reinhammar, B., Spiro, T.G., (1984) Biochemistry, 23, pp. 1084-1093
  • Nojiri, M., (2017) Metalloenzymes in Denitrification: Applications and Environmental Impacts, pp. 91-113. , ch. 5. London: The Royal Society of Chemistry
  • Nojiri, M., Koteishi, H., Nakagami, T., Kobayashi, K., Inoue, T., Yamaguchi, K., Suzuki, S., (2009) Nature, 462, pp. 117-120
  • Nojiri, M., Xie, Y., Inoue, T., Yamamoto, T., Matsumura, H., Kataoka, K., Deligeer Yamaguchi, K., Suzuki, S., (2007) Proc. Natl Acad. Sci. USA, 104, pp. 4315-4320
  • Okubo, T., Fukushima, S., Itakura, M., Oshima, K., Longtonglang, A., Teaumroong, N., Mitsui, H., Minamisawa, K., (2013) Appl. Environ. Microbiol, 79, pp. 2542-2551
  • Pérez-Henarejos, S.A., Alcaraz, L.A., Donaire, A., (2015) Arch. Biochem. Biophys, 584, pp. 134-148
  • Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., Ferrin, T.E., (2004) J. Comput. Chem, 25, pp. 1605-1612
  • Qin, X., Deng, L., Hu, C., Li, L., Chen, X., (2017) Chem. Eur. J, 23, pp. 14900-14910
  • Sharma, K.D., Loehr, T.M., Sanders-Loehr, J., Husain, M., Davidson, V.L., (1988) J. Biol. Chem, 263, pp. 3303-3306
  • Stoll, S., Schweiger, A., (2006) J. Magn. Reson, 178, pp. 42-55
  • Strange, R.W., Murphy, L.M., Dodd, F.E., Abraham, Z.H.L., Eady, R.R., Smith, B.E., Hasnain, S.S., (1999) J. Mol. Biol, 287, pp. 1001-1009
  • Studier, F.W., (2005) Protein Expr Purif, 41, pp. 207-234
  • Tocheva, E.I., Rosell, F.I., Mauk, A.G., Murphy, M.E.P., (2007) Biochemistry, 46, pp. 12366-12374
  • Tsuda, A., Ishikawa, R., Koteishi, H., Tange, K., Fukuda, Y., Kobayashi, K., Inoue, T., Nojiri, M., (2013) J. Biochem, (154), pp. 51-60
  • Vonrhein, C., Flensburg, C., Keller, P., Sharff, A., Smart, O., Paciorek, W., Womack, T., Bricogne, G., (2011) Acta Cryst D, 67, pp. 293-302
  • Whelan, S., Goldman, N., (2001) Mol. Biol. Evol, 18, pp. 691-699
  • Winn, M.D., Ballard, C.C., Cowtan, K.D., Dodson, E.J., Emsley, P., Evans, P.R., Keegan, R.M., Wilson, K.S., (2011) Acta Cryst D, 67, pp. 235-242
  • Yamaguchi, K., Kataoka, K., Kobayashi, M., Itoh, K., Fukui, A., Suzuki, S., (2004) Biochemistry, 43, pp. 14180-14188
  • Zumft, W.G., (1997) Microbiol. Mol. Biol. Rev, 61, pp. 533-616

Citas:

---------- APA ----------
Opperman, D.J., Murgida, D.H., Dalosto, S.D., Brondino, C.D. & Ferroni, F.M. (2019) . A three-domain copper-nitrite reductase with a unique sensing loop. IUCrJ, 6, 248-258.
http://dx.doi.org/10.1107/S2052252519000241
---------- CHICAGO ----------
Opperman, D.J., Murgida, D.H., Dalosto, S.D., Brondino, C.D., Ferroni, F.M. "A three-domain copper-nitrite reductase with a unique sensing loop" . IUCrJ 6 (2019) : 248-258.
http://dx.doi.org/10.1107/S2052252519000241
---------- MLA ----------
Opperman, D.J., Murgida, D.H., Dalosto, S.D., Brondino, C.D., Ferroni, F.M. "A three-domain copper-nitrite reductase with a unique sensing loop" . IUCrJ, vol. 6, 2019, pp. 248-258.
http://dx.doi.org/10.1107/S2052252519000241
---------- VANCOUVER ----------
Opperman, D.J., Murgida, D.H., Dalosto, S.D., Brondino, C.D., Ferroni, F.M. A three-domain copper-nitrite reductase with a unique sensing loop. IUCrJ. 2019;6:248-258.
http://dx.doi.org/10.1107/S2052252519000241