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| | ==X-ray structure of mutant N211D of bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)== | | ==X-ray structure of mutant N211D of bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)== |
| - | <StructureSection load='4dj4' size='340' side='right' caption='[[4dj4]], [[Resolution|resolution]] 2.35Å' scene=''> | + | <StructureSection load='4dj4' size='340' side='right'caption='[[4dj4]], [[Resolution|resolution]] 2.35Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4dj4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lycopersicon_esculentum Lycopersicon esculentum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DJ4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4dj4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DJ4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3sng|3sng]]</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4dj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dj4 OCA], [https://pdbe.org/4dj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dj4 RCSB], [https://www.ebi.ac.uk/pdbsum/4dj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dj4 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tbn1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4081 Lycopersicon esculentum])</td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4dj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dj4 OCA], [http://pdbe.org/4dj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dj4 RCSB], [http://www.ebi.ac.uk/pdbsum/4dj4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dj4 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [[https://www.uniprot.org/uniprot/Q0KFV0_SOLLC Q0KFV0_SOLLC]] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Lycopersicon esculentum]] | + | [[Category: Large Structures]] |
| - | [[Category: Dohnalek, J]] | + | [[Category: Solanum lycopersicum]] |
| - | [[Category: Duskova, J]] | + | [[Category: Dohnalek J]] |
| - | [[Category: Hasek, J]] | + | [[Category: Duskova J]] |
| - | [[Category: Koval, T]] | + | [[Category: Hasek J]] |
| - | [[Category: Lipovova, P]] | + | [[Category: Koval T]] |
| - | [[Category: Matousek, J]] | + | [[Category: Lipovova P]] |
| - | [[Category: Podzimek, T]] | + | [[Category: Matousek J]] |
| - | [[Category: Skalova, T]] | + | [[Category: Podzimek T]] |
| - | [[Category: Stepankova, A]] | + | [[Category: Skalova T]] |
| - | [[Category: 3'-nucleotidase]]
| + | [[Category: Stepankova A]] |
| - | [[Category: Bi-functional]]
| + | |
| - | [[Category: Cytosol membrane associated]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Mainly alpha helical]]
| + | |
| - | [[Category: Nuclease]]
| + | |
| - | [[Category: Trinuclear metal centre]]
| + | |
| Structural highlights
4dj4 is a 2 chain structure with sequence from Solanum lycopersicum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
[Q0KFV0_SOLLC]
Publication Abstract from PubMed
Type I plant nucleases play an important role in apoptotic processes and cell senescence. Recently, they have also been indicated to be potent anticancer agents in in vivo studies. The first structure of tomato nuclease I (TBN1) has been determined, its oligomerization and activity profiles have been analyzed and its unexpected activity towards phospholipids has been discovered, and conclusions are drawn regarding its catalytic mechanism. The structure-solution process required X-ray diffraction data from two crystal forms. The first form was used for phase determination; the second form was used for model building and refinement. TBN1 is mainly alpha-helical and is stabilized by four disulfide bridges. Three observed oligosaccharides are crucial for its stability and solubility. The active site is localized at the bottom of the positively charged groove and contains a zinc cluster that is essential for enzymatic activity. An equilibrium between monomers, dimers and higher oligomers of TBN1 was observed in solution. Principles of the reaction mechanism of the phosphodiesterase activity are suggested, with central roles for the zinc cluster, the nucleobase-binding pocket (Phe-site) and Asp70, Arg73 and Asn167. Based on the distribution of surface residues, possible binding sites for dsDNA and other nucleic acids with secondary structure were identified. The phospholipase activity of TBN1, which is reported for the first time for a nuclease, significantly broadens the substrate promiscuity of the enzyme, and the resulting release of diacylglycerol, which is an important second messenger, can be related to the role of TBN1 in apoptosis.
Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis.,Koval' T, Lipovova P, Podzimek T, Matousek J, Duskova J, Skalova T, Stepankova A, Hasek J, Dohnalek J Acta Crystallogr D Biol Crystallogr. 2013 Feb;69(Pt 2):213-26. doi:, 10.1107/S0907444912043697. Epub 2013 Jan 16. PMID:23385457[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Koval' T, Lipovova P, Podzimek T, Matousek J, Duskova J, Skalova T, Stepankova A, Hasek J, Dohnalek J. Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis. Acta Crystallogr D Biol Crystallogr. 2013 Feb;69(Pt 2):213-26. doi:, 10.1107/S0907444912043697. Epub 2013 Jan 16. PMID:23385457 doi:http://dx.doi.org/10.1107/S0907444912043697
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