3sng: Difference between revisions

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<StructureSection load='3sng' size='340' side='right'caption='[[3sng]], [[Resolution|resolution]] 2.16&Aring;' scene=''>
<StructureSection load='3sng' size='340' side='right'caption='[[3sng]], [[Resolution|resolution]] 2.16&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3sng]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lycopersicon_esculentum Lycopersicon esculentum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SNG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SNG FirstGlance]. <br>
<table><tr><td colspan='2'>[[3sng]] is a 1 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=3SNG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SNG FirstGlance]. <br>
</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=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.16&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tbn1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4081 Lycopersicon esculentum])</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=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=3sng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sng OCA], [https://pdbe.org/3sng PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sng RCSB], [https://www.ebi.ac.uk/pdbsum/3sng PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sng ProSAT]</span></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=3sng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sng OCA], [https://pdbe.org/3sng PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sng RCSB], [https://www.ebi.ac.uk/pdbsum/3sng PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sng ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/Q0KFV0_SOLLC Q0KFV0_SOLLC]
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<ref>PMID:23385457</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3sng" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Lycopersicon esculentum]]
[[Category: Solanum lycopersicum]]
[[Category: Dohnalek, J]]
[[Category: Dohnalek J]]
[[Category: Duskova, J]]
[[Category: Duskova J]]
[[Category: Hasek, J]]
[[Category: Hasek J]]
[[Category: Koval, T]]
[[Category: Koval T]]
[[Category: Lipovova, P]]
[[Category: Lipovova P]]
[[Category: Matousek, J]]
[[Category: Matousek J]]
[[Category: Podzimek, T]]
[[Category: Podzimek T]]
[[Category: Skalova, T]]
[[Category: Skalova T]]
[[Category: Stepankova, A]]
[[Category: Stepankova A]]
[[Category: 3'-nucleotidase]]
[[Category: Bi-functional]]
[[Category: Cytosol membrane associated]]
[[Category: Endonuclease]]
[[Category: Hydrolase]]
[[Category: Mainly alpha helical]]
[[Category: Mononucleotide]]
[[Category: Nucleic acid]]
[[Category: Trinuclear metal centre]]

Revision as of 13:02, 14 March 2024

X-ray structure of fully glycosylated bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)

3sng, resolution 2.16Å

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