1kqq: Difference between revisions

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-{{Seed}}
-[[Image:1kqq.png|left|200px]]
-<!--
+==Solution Structure of the Dead ringer ARID-DNA Complex==
-The line below this paragraph, containing "STRUCTURE_1kqq", creates the "Structure Box" on the page.
+<StructureSection load='1kqq' size='340' side='right'caption='[[1kqq]]' 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'>[[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>
-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">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>
-{{STRUCTURE_1kqq|  PDB=1kqq  |  SCENE=  }}
+</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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_11867548}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1kqq" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 11867548 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11867548}}
+__TOC__
+</StructureSection>
-==About this Structure==
-KQQ is a [[Single protein]] structure of 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].
-==Reference==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/11867548 11867548]
 [[Category: Drosophila melanogaster]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Clubb, R T.]]
+[[Category: Clubb RT]]
-[[Category: Daughdrill, G W.]]
+[[Category: Daughdrill GW]]
-[[Category: Ford, J.]]
+[[Category: Ford J]]
-[[Category: Iwahara, J.]]
+[[Category: Iwahara J]]
-[[Category: Iwahara, M.]]
+[[Category: Iwahara M]]
-[[Category: Arid]]
-[[Category: Protein-dna complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  2 10:47:37 2008''