4JDG
Structure of Tomato Bifunctional Nuclease TBN1, variant N211D
Summary for 4JDG
| Entry DOI | 10.2210/pdb4jdg/pdb |
| Related | 3SNG 4DJ4 |
| Descriptor | Nuclease, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (6 entities in total) |
| Functional Keywords | mainly alpha helical, trinuclear metal centre, multi-functional, nuclease, 3'-nucleotidase, hydrolase, glycosylated, cytosol membrane associated |
| Biological source | Solanum lycopersicum (tomato) |
| Total number of polymer chains | 1 |
| Total formula weight | 33273.94 |
| Authors | Stransky, J.,Dohnalek, J.,Koval, T.,Podzimek, T.,Lipovova, P.,Matousek, J. (deposition date: 2013-02-25, release date: 2014-02-26, Last modification date: 2024-10-30) |
| Primary citation | Stransky, J.,Koval, T.,Podzimek, T.,Tycova, A.,Lipovova, P.,Matousek, J.,Kolenko, P.,Fejfarova, K.,Duskova, J.,Skalova, T.,Hasek, J.,Dohnalek, J. Phosphate binding in the active centre of tomato multifunctional nuclease TBN1 and analysis of superhelix formation by the enzyme Acta Crystallogr.,Sect.F, 71:1408-1415, 2015 Cited by PubMed Abstract: Tomato multifunctional nuclease TBN1 belongs to the type I nuclease family, which plays an important role in apoptotic processes and cell senescence in plants. The newly solved structure of the N211D mutant is reported. Although the main crystal-packing motif (the formation of superhelices) is conserved, the details differ among the known structures. A phosphate ion was localized in the active site of the enzyme. The binding of the surface loop to the active centre is stabilized by the phosphate ion, which correlates with the observed aggregation of TBN1 in phosphate buffer. The conserved binding of the surface loop to the active centre suggests biological relevance of the contact in a regulatory function or in the formation of oligomers. PubMed: 26527269DOI: 10.1107/S2053230X15018324 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.74 Å) |
Structure validation
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