2hdd: Difference between revisions

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<StructureSection load='2hdd' size='340' side='right'caption='[[2hdd]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='2hdd' size='340' side='right'caption='[[2hdd]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2hdd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HDD FirstGlance]. <br>
<table><tr><td colspan='2'>[[2hdd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HDD FirstGlance]. <br>
</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=2hdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hdd OCA], [https://pdbe.org/2hdd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hdd RCSB], [https://www.ebi.ac.uk/pdbsum/2hdd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hdd ProSAT]</span></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</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=2hdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hdd OCA], [https://pdbe.org/2hdd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hdd RCSB], [https://www.ebi.ac.uk/pdbsum/2hdd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hdd ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/HMEN_DROME HMEN_DROME]] This protein specifies the body segmentation pattern. It is required for the development of the central nervous system. Transcriptional regulator that represses activated promoters. Wg signaling operates by inactivating the SGG repression of EN autoactivation.  
[https://www.uniprot.org/uniprot/HMEN_DROME HMEN_DROME] This protein specifies the body segmentation pattern. It is required for the development of the central nervous system. Transcriptional regulator that represses activated promoters. Wg signaling operates by inactivating the SGG repression of EN autoactivation.
== 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=2hdd 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=2hdd ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
BACKGROUND: The homeodomain is one of the key DNA-binding motifs used in eukaryotic gene regulation, and homeodomain proteins play critical roles in development. The residue at position 50 of many homeodomains appears to determine the differential DNA-binding specificity, helping to distinguish among binding sites of the form TAATNN. However, the precise role(s) of residue 50 in the differential recognition of alternative sites has not been clear. None of the previously determined structures of homeodomain-DNA complexes has shown evidence for a stable hydrogen bond between residue 50 and a base, and there has been much discussion, based in part on NMR studies, about the potential importance of water-mediated contacts. This study was initiated to help clarify some of these issues. RESULTS: The crystal structure of a complex containing the engrailed Gln50--&gt;Lys variant (QK50) with its optimal binding site TAATCC (versus TAATTA for the wild-type protein) has been determined at 1.9 A resolution. The overall structure of the QK50 variant is very similar to that of the wild-type complex, but the sidechain of Lys50 projects directly into the major groove and makes several hydrogen bonds to the O6 and N7 atoms of the guanines at base pairs 5 and 6. Lys50 also makes an additional water-mediated contact with the guanine at base pair 5 and has an alternative conformation that allows a hydrogen bond with the O4 of the thymine at base pair 4. CONCLUSIONS: The structural context provided by the folding and docking of the engrailed homeodomain allows Lys50 to make remarkably favorable contacts with the guanines at base pairs 5 and 6 of the binding site. Although many different residues occur at position 50 in different homeodomains, and although numerous position 50 variants have been constructed, the most striking examples of altered specificity usually involve introducing or removing a lysine sidechain from position 50. This high-resolution structure also confirms the critical role of Asn51 in homeodomain-DNA recognition and further clarifies the roles of water molecules near residues 50 and 51.
Engrailed (Gln50--&gt;Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity.,Tucker-Kellogg L, Rould MA, Chambers KA, Ades SE, Sauer RT, Pabo CO Structure. 1997 Aug 15;5(8):1047-54. PMID:9309220<ref>PMID:9309220</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2hdd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Drome]]
[[Category: Drosophila melanogaster]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Ades, S E]]
[[Category: Ades SE]]
[[Category: Chambers, K A]]
[[Category: Chambers KA]]
[[Category: Pabo, C O]]
[[Category: Pabo CO]]
[[Category: Rould, M A]]
[[Category: Rould MA]]
[[Category: Sauer, R T]]
[[Category: Sauer RT]]
[[Category: Tucker-Kellogg, L]]
[[Category: Tucker-Kellogg L]]
[[Category: Dna binding]]
[[Category: Transcription-dna complex]]

Latest revision as of 12:32, 14 February 2024

ENGRAILED HOMEODOMAIN Q50K VARIANT DNA COMPLEXENGRAILED HOMEODOMAIN Q50K VARIANT DNA COMPLEX

Structural highlights

2hdd is a 4 chain structure with sequence from Drosophila melanogaster. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HMEN_DROME This protein specifies the body segmentation pattern. It is required for the development of the central nervous system. Transcriptional regulator that represses activated promoters. Wg signaling operates by inactivating the SGG repression of EN autoactivation.

Evolutionary Conservation

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

2hdd, resolution 1.90Å

Drag the structure with the mouse to rotate

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OCA
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