1kqq: Difference between revisions

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-[[Image:1kqq.png|left|200px]]
-{{STRUCTURE_1kqq|  PDB=1kqq  |  SCENE=  }}
+==Solution Structure of the Dead ringer ARID-DNA Complex==
+<StructureSection load='1kqq' size='340' side='right'caption='[[1kqq]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1kqq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KQQ FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1kqq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqq OCA], [https://pdbe.org/1kqq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kqq RCSB], [https://www.ebi.ac.uk/pdbsum/1kqq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kqq ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DRI_DROME DRI_DROME] Transcription factor which is a downstream target of gcm and repo. Directly or indirectly activates the transcription of locos and pros, which are essential for the development of some glial cells. Plays an essential role in defining the cell shape and migration characteristics of longitudinal glia that enable them to establish a normal axon scaffold.<ref>PMID:12620977</ref> <ref>PMID:15576402</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/kq/1kqq_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=1kqq ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The AT-rich interaction domain (ARID) is a DNA-binding module found in many eukaryotic transcription factors. Using NMR spectroscopy, we have determined the first ever three-dimensional structure of an ARID--DNA complex (mol. wt 25.7 kDa) formed by Dead ringer from Drosophila melanogaster. ARIDs recognize DNA through a novel mechanism involving major groove immobilization of a large loop that connects the helices of a non-canonical helix-turn-helix motif, and through a concomitant structural rearrangement that produces stabilizing contacts from a beta-hairpin. Dead ringer's preference for AT-rich DNA originates from three positions within the ARID fold that form energetically significant contacts to an adenine-thymine base step. Amino acids that dictate binding specificity are not highly conserved, suggesting that ARIDs will bind to a range of nucleotide sequences. Extended ARIDs, found in several sequence-specific transcription factors, are distinguished by the presence of a C-terminal helix that may increase their intrinsic affinity for DNA. The prevalence of serine amino acids at all specificity determining positions suggests that ARIDs within SWI/SNF-related complexes will interact with DNA non-sequence specifically.
-===Solution Structure of the Dead ringer ARID-DNA Complex===
+The structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA.,Iwahara J, Iwahara M, Daughdrill GW, Ford J, Clubb RT EMBO J. 2002 Mar 1;21(5):1197-209. PMID:11867548<ref>PMID:11867548</ref>
-{{ABSTRACT_PUBMED_11867548}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1kqq" style="background-color:#fffaf0;"></div>
-[[1kqq]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQQ OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:011867548</ref><ref group="xtra">PMID:011845213</ref><references group="xtra"/>
+</StructureSection>
 [[Category: Drosophila melanogaster]]
-[[Category: Clubb, R T.]]
+[[Category: Large Structures]]
-[[Category: Daughdrill, G W.]]
+[[Category: Clubb RT]]
-[[Category: Ford, J.]]
+[[Category: Daughdrill GW]]
-[[Category: Iwahara, J.]]
+[[Category: Ford J]]
-[[Category: Iwahara, M.]]
+[[Category: Iwahara J]]
-[[Category: Arid]]
+[[Category: Iwahara M]]
-[[Category: Protein-dna complex]]
-[[Category: Transcription-dna complex]]