3dti: Difference between revisions

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-{{Seed}}
-[[Image:3dti.jpg|left|200px]]
-<!--
+==Crystal structure of the IRRE protein, a central regulator of DNA damage repair in deinococcaceae==
-The line below this paragraph, containing "STRUCTURE_3dti", creates the "Structure Box" on the page.
+<StructureSection load='3dti' size='340' side='right'caption='[[3dti]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3dti]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_deserti Deinococcus deserti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DTI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DTI FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3dti|  PDB=3dti  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dti FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dti OCA], [https://pdbe.org/3dti PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dti RCSB], [https://www.ebi.ac.uk/pdbsum/3dti PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dti ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/IRRE_DEIDV IRRE_DEIDV] Plays a central regulatory role in DNA repair and protection pathways in response to radiation stress. Acts as a site-specific metalloprotease that cleaves and inactivates the repressor proteins DdrOC and DdrOP3, resulting in induced expression of genes required for DNA repair and cell survival after exposure to radiation.<ref>PMID:25170972</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dt/3dti_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3dti ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Deinococcaceae are famous for their extreme radioresistance. Transcriptome analysis in Deinococcus radiodurans revealed a group of genes up-regulated in response to desiccation and ionizing radiation. IrrE, a novel protein initially found in D. radiodurans, was shown to be a positive regulator of some of these genes. Deinococcus deserti irrE is able to restore radioresistance in a D. radiodurans DeltairrE mutant. The D. deserti IrrE crystal structure reveals a unique combination of three domains: one zinc peptidase-like domain, one helix-turn-helix motif and one GAF-like domain. Mutant analysis indicates that the first and third domains are critical regions for radiotolerance. In particular, mutants affected in the putative zinc-binding site are as sensitive to gamma and UV irradiation as the DeltairrE bacteria, and radioresistance is strongly decreased with the H217L mutation present in the C-terminal domain. In addition, modeling of IrrE-DNA interaction suggests that the observed IrrE structure may not bind double-stranded DNA through its central helix-turn-helix motif and that IrrE is not a classic transcriptional factor that activates gene expression by its direct binding to DNA. We propose that the putative protease activity of IrrE could be a key element of transcription enhancement and that a more classic transcription factor, possibly an IrrE substrate, would link IrrE to transcription of genes specifically involved in radioresistance.
-===Crystal structure of the IRRE protein, a central regulator of DNA damage repair in deinococcaceae===
+Crystal Structure of the IrrE Protein, a Central Regulator of DNA Damage Repair in Deinococcaceae.,Vujicic-Zagar A, Dulermo R, Le Gorrec M, Vannier F, Servant P, Sommer S, de Groot A, Serre L J Mol Biol. 2009 Jan 3. PMID:19150362<ref>PMID:19150362</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_19150362}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3dti" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19150362 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19150362}}
+__TOC__
+</StructureSection>
-==About this Structure==
-DTI is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Deinococcus_deserti Deinococcus deserti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DTI OCA].
-==Reference==
-<ref group="xtra">PMID:19150362</ref><references group="xtra"/>
 [[Category: Deinococcus deserti]]
-[[Category: Dulermo, R.]]
+[[Category: Large Structures]]
-[[Category: Gorrec, M Le.]]
+[[Category: De Groot A]]
-[[Category: Groot, A De.]]
+[[Category: Dulermo R]]
-[[Category: Serre, L.]]
+[[Category: Le Gorrec M]]
-[[Category: Servant, P.]]
+[[Category: Serre L]]
-[[Category: Sommer, S.]]
+[[Category: Servant P]]
-[[Category: Vannier, F.]]
+[[Category: Sommer S]]
-[[Category: Vujicic-Zagar, A.]]
+[[Category: Vannier F]]
-[[Category: Deinococcus]]
+[[Category: Vujicic-Zagar A]]
-[[Category: Gene regulation]]
-[[Category: Irre]]
-[[Category: Metallopeptidase]]
-[[Category: Radiotolerance]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 11 12:40:25 2009''