1zq3: Difference between revisions
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==NMR Solution Structure of the Bicoid Homeodomain Bound to the Consensus DNA Binding Site TAATCC== | ==NMR Solution Structure of the Bicoid Homeodomain Bound to the Consensus DNA Binding Site TAATCC== | ||
<StructureSection load='1zq3' size='340' side='right' caption='[[1zq3 | <StructureSection load='1zq3' size='340' side='right'caption='[[1zq3]]' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1zq3]] is a 3 chain structure with sequence from [ | <table><tr><td colspan='2'>[[1zq3]] 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=1ZQ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZQ3 FirstGlance]. <br> | ||
</td></tr><tr id=' | </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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1zq3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zq3 OCA], [https://pdbe.org/1zq3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zq3 RCSB], [https://www.ebi.ac.uk/pdbsum/1zq3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zq3 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/BCD_DROME BCD_DROME] Segment polarity protein that provides positional cues for the development of head and thoracic segments. Regulates the expression of zygotic genes, possibly through its homeodomain, and inhibits the activity of other maternal gene products. May also bind RNA. Interacts with Bin1 to repress transcription of bicoid target genes in the anterior tip of the embryo; a process known as retraction. | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zq/1zq3_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zq/1zq3_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=1zq3 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 31: | Line 32: | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Drosophila melanogaster]] | ||
[[Category: Baird-Titus | [[Category: Large Structures]] | ||
[[Category: Clark-Baldwin | [[Category: Baird-Titus JM]] | ||
[[Category: Ma | [[Category: Clark-Baldwin K]] | ||
[[Category: Rance | [[Category: Ma J]] | ||
[[Category: Vrushank | [[Category: Rance M]] | ||
[[Category: Vrushank D]] | |||
Latest revision as of 11:12, 15 May 2024
NMR Solution Structure of the Bicoid Homeodomain Bound to the Consensus DNA Binding Site TAATCCNMR Solution Structure of the Bicoid Homeodomain Bound to the Consensus DNA Binding Site TAATCC
Structural highlights
FunctionBCD_DROME Segment polarity protein that provides positional cues for the development of head and thoracic segments. Regulates the expression of zygotic genes, possibly through its homeodomain, and inhibits the activity of other maternal gene products. May also bind RNA. Interacts with Bin1 to repress transcription of bicoid target genes in the anterior tip of the embryo; a process known as retraction. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe solution structure of the homeodomain of the Drosophila morphogenic protein Bicoid (Bcd) complexed with a TAATCC DNA site is described. Bicoid is the only known protein that uses a homeodomain to regulate translation, as well as transcription, by binding to both RNA and DNA during early Drosophila development; in addition, the Bcd homeodomain can recognize an array of different DNA sites. The dual functionality and broad recognition capabilities signify that the Bcd homeodomain may possess unique structural/dynamic properties. Bicoid is the founding member of the K50 class of homeodomain proteins, containing a lysine residue at the critical 50th position (K50) of the homeodomain sequence, a residue required for DNA and RNA recognition; Bcd also has an arginine residue at the 54th position (R54), which is essential for RNA recognition. Bcd is the only known homeodomain with the K50/R54 combination of residues. The Bcd structure indicates that this homeodomain conforms to the conserved topology of the homeodomain motif, but exhibits a significant variation from other homeodomain structures at the end of helix 1. A key result is the observation that the side-chains of the DNA-contacting residues K50, N51 and R54 all show strong signs of flexibility in the protein-DNA interface. This finding is supportive of the adaptive-recognition theory of protein-DNA interactions. The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site.,Baird-Titus JM, Clark-Baldwin K, Dave V, Caperelli CA, Ma J, Rance M J Mol Biol. 2006 Mar 10;356(5):1137-51. Epub 2005 Dec 22. PMID:16406070[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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