|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | + | |
| | ==Structure of Tomato Bifunctional Nuclease TBN1, variant N211D== | | ==Structure of Tomato Bifunctional Nuclease TBN1, variant N211D== |
| - | <StructureSection load='4jdg' size='340' side='right' caption='[[4jdg]], [[Resolution|resolution]] 2.74Å' scene=''> | + | <StructureSection load='4jdg' size='340' side='right'caption='[[4jdg]], [[Resolution|resolution]] 2.74Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4jdg]] is a 1 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=4JDG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JDG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4jdg]] 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=4JDG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JDG 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=PO4:PHOSPHATE+ION'>PO4</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]] 2.74Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3sng|3sng]], [[4dj4|4dj4]]</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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=4jdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jdg OCA], [https://pdbe.org/4jdg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jdg RCSB], [https://www.ebi.ac.uk/pdbsum/4jdg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jdg ProSAT]</span></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=4jdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jdg OCA], [http://pdbe.org/4jdg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jdg RCSB], [http://www.ebi.ac.uk/pdbsum/4jdg PDBsum]</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 == |
| Line 21: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Lycopersicon esculentum]] | + | [[Category: Large Structures]] |
| - | [[Category: Dohnalek, J]] | + | [[Category: Solanum lycopersicum]] |
| - | [[Category: Koval, T]] | + | [[Category: Dohnalek J]] |
| - | [[Category: Lipovova, P]] | + | [[Category: Koval T]] |
| - | [[Category: Matousek, J]] | + | [[Category: Lipovova P]] |
| - | [[Category: Podzimek, T]] | + | [[Category: Matousek J]] |
| - | [[Category: Stransky, J]] | + | [[Category: Podzimek T]] |
| - | [[Category: 3'-nucleotidase]]
| + | [[Category: Stransky J]] |
| - | [[Category: Cytosol membrane associated]]
| + | |
| - | [[Category: Glycosylated]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Mainly alpha helical]]
| + | |
| - | [[Category: Multi-functional]]
| + | |
| - | [[Category: Nuclease]]
| + | |
| - | [[Category: Trinuclear metal centre]]
| + | |
| Structural highlights
4jdg is a 1 chain structure with sequence from Solanum lycopersicum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.74Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
Q0KFV0_SOLLC
Publication Abstract from PubMed
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.
Phosphate binding in the active centre of tomato multifunctional nuclease TBN1 and analysis of superhelix formation by the enzyme.,Stransky J, Koval' T, Podzimek T, Tycova A, Lipovova P, Matousek J, Kolenko P, Fejfarova K, Duskova J, Skalova T, Hasek J, Dohnalek J Acta Crystallogr F Struct Biol Commun. 2015 Nov 1;71(Pt 11):1408-15. doi:, 10.1107/S2053230X15018324. Epub 2015 Oct 23. PMID:26527269[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ 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 F Struct Biol Commun. 2015 Nov 1;71(Pt 11):1408-15. doi:, 10.1107/S2053230X15018324. Epub 2015 Oct 23. PMID:26527269 doi:http://dx.doi.org/10.1107/S2053230X15018324
|
