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| | <StructureSection load='6iz2' size='340' side='right'caption='[[6iz2]], [[Resolution|resolution]] 2.07Å' scene=''> | | <StructureSection load='6iz2' size='340' side='right'caption='[[6iz2]], [[Resolution|resolution]] 2.07Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6iz2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IZ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IZ2 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6iz2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IZ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IZ2 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.069Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DR_0053 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6iz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iz2 OCA], [http://pdbe.org/6iz2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iz2 RCSB], [http://www.ebi.ac.uk/pdbsum/6iz2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iz2 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=6iz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iz2 OCA], [https://pdbe.org/6iz2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6iz2 RCSB], [https://www.ebi.ac.uk/pdbsum/6iz2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6iz2 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/Q9RY97_DEIRA Q9RY97_DEIRA] |
| - | Deinococcus radiodurans is an extremophilic bacterium well-known for its extraordinary resistance to ionizing radiation and other DNA damage- and oxidative stress-generating agents. In addition to its efficient DNA damage repair and oxidative stress resistance mechanisms, protein family expansions and stress-induced genes/proteins are also regarded as important components that add to the robustness of this bacterium. D. radiodurans encodes specific expansions of 13 DinB/YfiT homologs, which is a relatively large number when compared to those found in Gram-positive bacteria. In this study, we investigated the expression profiles of 13 dinB genes after gamma-irradiation, mitomycin C and H2O2 treatment. dr0053 had the highest expression levels after DNA-damage inducing gamma-irradiation and MMC treatment, increasing approximately 200-fold and approximately 16-fold, respectively. We also determined the crystal structure of DR0053 at 2.07A resolution. DR0053 adopted a typical four-helix bundle structure that is characteristic of DinB/YfiT proteins. A putative metal binding site was occupied by zinc even though the highly conserved His triad of DinB/YfiT proteins was replaced by Glu-Asn-His.
| + | |
| - | | + | |
| - | Crystal structure of the highly radiation-inducible DinB/YfiT superfamily protein DR0053 from Deinococcus radiodurans R1.,Zhang J, Zhao L, Seo HS, Jung JH, Choi JI, Kim MK, Lim S Biochem Biophys Res Commun. 2019 May 28;513(2):354-359. doi:, 10.1016/j.bbrc.2019.03.209. Epub 2019 Apr 5. PMID:30961930<ref>PMID:30961930</ref>
| + | |
| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 6iz2" style="background-color:#fffaf0;"></div>
| + | |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Deira]] | + | [[Category: Deinococcus radiodurans R1]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Kim, M K]] | + | [[Category: Kim M-K]] |
| - | [[Category: Zhang, J]] | + | [[Category: Zhang J]] |
| - | [[Category: Zhao, L]] | + | [[Category: Zhao L]] |
| - | [[Category: Damage response]]
| + | |
| - | [[Category: Four helix bundle]]
| + | |
| - | [[Category: Unknown function]]
| + | |
