Structural analysis of a recombinant plant bifunctional nuclease TBN1


T. Koval1, P. Lipovova3, T. Podzimek3,4, J. Matousek4, J. Duskova2, T. Skalova2,  A. Stepankova2, J. Hasek2 and J. Dohnalek1,2


1Institute of Physics, Academy of Sciences of the Czech Republic,v.v.i., Na Slovance 2,182 21 Praha 6, Czech Republic,

2Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic,v.v.i., Heyrovskeho nam. 2, 162 06 Praha 6, Czech Republic

3Institute of Chemical Technology, Technicka 5, 166 28 Praha 6, Czech Republic

4Institute of Plant Molecular Biology, Biology Centre, Academy of Sciences of the Czech Republic,v.v.i., Branisovska 31, 370 05 Ceske Budejovice, Czech Republic


Bifunctional nuclease TBN1 (sequence accession no. AM238701) from Solanum lycopersicum (red tomato) is a Zn2+- dependent plant glycoprotein composed of 277 amino acids with a molecular mass of 31.6 kDa (about 37 kDa when glycosylated). TBN1 belongs to plant nuclease I group and plays a considerable role in specific apoptotic functions, vascular system development, stress response and tissue differentiation in plants [1]. In addition, TBN1 exhibits anticancerogenic properties [2]. Therefore, a detailed structural study of this enzyme can contribute to development of new drugs for cancer, bacterial and viral disease treatment. Nuclease P1 from Penicillium citrinum with 24% sequence identity, the structure of which is known (PDB ID 1ak0) [3], is probably the closest structural homologue of TBN1.

      Heterologous expression of TBN1 in tobacco leaves yields amounts and quality of the enzyme suitable for structural studies. Crystals with sufficient quality for X-ray diffraction analysis can be obtained. The first diffraction experiments were performed using an in house Gemini Enhanced Ultra diffractometer with the Atlas CCD detector (Oxford Diffraction) and three different crystal morphologies were identified (orthorhombic, rhombohedral and trigonal). Datasets for structural analysis were collected at the synchrotron radiation source BESSY II (Helmholtz-Zentrum Berlin), beam line MX-14-1, with a MARmosaic CCD detector. Presence of zinc in the protein was confirmed by X-ray fluorescence and an absorption edge scan and two MAD datasets (for a rhombohedral and a trigonal crystal) were collected. The phase problem was solved using the SHELXC, D and E program suite [4]. The TBN1 structure resembles some features of P1 nuclease with differences near the active site and in the glycosylation pattern.


The work on this project was supported by the Czech Science Foundation, project no. 310/09/1407. We also thank the Grant Agency of the Czech Republic, project no. 202/06/0757 and project no.521/09/1214 and by the EC under ELISA grant agreement number 226716 (synchrotron access, projects 09.2.90262 and 10.1.91347). We also gratefully acknowledge support from Praemium Academiae of AS CR, Institution research plan AVOZ10100521 of the Institute of Physics, Institution research plan AV0Z50510513 of the Institute of Plant Molecular Biology, Biology Centre. The authors wish to thank Dr. U. Müller of the Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15 for support at the beam line.

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