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==Solution Structure of the Dead ringer ARID-DNA Complex==
==Solution Structure of the Dead ringer ARID-DNA Complex==
<StructureSection load='1kqq' size='340' side='right'caption='[[1kqq]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
<StructureSection load='1kqq' size='340' side='right'caption='[[1kqq]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1kqq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Drome Drome]. 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>
<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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dri ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr>
</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>
<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>
</table>
== Function ==
== 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>
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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].
</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="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.
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>
<div class="pdbe-citations 1kqq" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Drome]]
[[Category: Drosophila melanogaster]]
[[Category: Large Structures]]
[[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]]
[[Category: Transcription-dna complex]]

Revision as of 11:02, 3 April 2024

Solution Structure of the Dead ringer ARID-DNA ComplexSolution Structure of the Dead ringer ARID-DNA Complex

Structural highlights

1kqq is a 3 chain structure with sequence from Drosophila melanogaster. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1] [2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Shandala T, Takizawa K, Saint R. The dead ringer/retained transcriptional regulatory gene is required for positioning of the longitudinal glia in the Drosophila embryonic CNS. Development. 2003 Apr;130(8):1505-13. PMID:12620977
  2. ↑ Ditch LM, Shirangi T, Pitman JL, Latham KL, Finley KD, Edeen PT, Taylor BJ, McKeown M. Drosophila retained/dead ringer is necessary for neuronal pathfinding, female receptivity and repression of fruitless independent male courtship behaviors. Development. 2005 Jan;132(1):155-64. Epub 2004 Dec 2. PMID:15576402 doi:http://dx.doi.org/10.1242/dev.01568
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