2r5y: Difference between revisions

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-[[Image:2r5y.jpg|left|200px]]
- {{Structure
+==Structure of Scr/Exd complex bound to a consensus Hox-Exd site==
-|PDB= 2r5y |SIZE=350|CAPTION= <scene name='initialview01'>2r5y</scene>, resolution 2.60&Aring;
+<StructureSection load='2r5y' size='340' side='right'caption='[[2r5y]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
+<table><tr><td colspan='2'>[[2r5y]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R5Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R5Y FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
-|GENE= Scr ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster]), exd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster])
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2r5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r5y OCA], [https://pdbe.org/2r5y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r5y RCSB], [https://www.ebi.ac.uk/pdbsum/2r5y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r5y ProSAT]</span></td></tr>
-|DOMAIN=
+</table>
-|RELATEDENTRY=[[1b8i|1B8I]], [[2r5z|2R5Z]]
+== Function ==
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r5y OCA], [http://www.ebi.ac.uk/pdbsum/2r5y PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2r5y RCSB]</span>
+[https://www.uniprot.org/uniprot/SCR_DROME SCR_DROME] Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Controls the segmental transformation of the first to the second thoracic segment (prothorax to mesothorax) and of the labial palps into maxillary palps. In embryo, required for fusion of labial lobes and development of the T1 denticle belt. In adult, expression in the head is necessary for proper development of the labium. In the first thoracic segment of the adult, required for proper development of the sex comb and to suppress improper prothoracic wing development.<ref>PMID:1743486</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/r5/2r5y_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=2r5y ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The recognition of specific DNA-binding sites by transcription factors is a critical yet poorly understood step in the control of gene expression. Members of the Hox family of transcription factors bind DNA by making nearly identical major groove contacts via the recognition helices of their homeodomains. In vivo specificity, however, often depends on extended and unstructured regions that link Hox homeodomains to a DNA-bound cofactor, Extradenticle (Exd). Using a combination of structure determination, computational analysis, and in vitro and in vivo assays, we show that Hox proteins recognize specific Hox-Exd binding sites via residues located in these extended regions that insert into the minor groove but only when presented with the correct DNA sequence. Our results suggest that these residues, which are conserved in a paralog-specific manner, confer specificity by recognizing a sequence-dependent DNA structure instead of directly reading a specific DNA sequence.
-'''Structure of Scr/Exd complex bound to a consensus Hox-Exd site'''
+Functional specificity of a Hox protein mediated by the recognition of minor groove structure.,Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS Cell. 2007 Nov 2;131(3):530-43. PMID:17981120<ref>PMID:17981120</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2r5y" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-The recognition of specific DNA-binding sites by transcription factors is a critical yet poorly understood step in the control of gene expression. Members of the Hox family of transcription factors bind DNA by making nearly identical major groove contacts via the recognition helices of their homeodomains. In vivo specificity, however, often depends on extended and unstructured regions that link Hox homeodomains to a DNA-bound cofactor, Extradenticle (Exd). Using a combination of structure determination, computational analysis, and in vitro and in vivo assays, we show that Hox proteins recognize specific Hox-Exd binding sites via residues located in these extended regions that insert into the minor groove but only when presented with the correct DNA sequence. Our results suggest that these residues, which are conserved in a paralog-specific manner, confer specificity by recognizing a sequence-dependent DNA structure instead of directly reading a specific DNA sequence.
+*[[Hox protein|Hox protein]]
+== References ==
-==About this Structure==
+<references/>
-R5Y is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R5Y OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Functional specificity of a Hox protein mediated by the recognition of minor groove structure., Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS, Cell. 2007 Nov 2;131(3):530-43. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17981120 17981120]
 [[Category: Drosophila melanogaster]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Aggarwal, A K.]]
+[[Category: Synthetic construct]]
-[[Category: Jain, R.]]
+[[Category: Aggarwal AK]]
-[[Category: Passner, J M.]]
+[[Category: Jain R]]
-[[Category: developmental protein]]
+[[Category: Passner JM]]
-[[Category: dna-binding]]
-[[Category: homeobox]]
-[[Category: homeodomain]]
-[[Category: homeotic protein]]
-[[Category: nucleus]]
-[[Category: specificity]]
-[[Category: transcription]]
-[[Category: transcription regulation]]
-[[Category: transcription/dna complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:57:01 2008''