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New page: left|200px<br /><applet load="1ahd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ahd" /> '''DETERMINATION OF THE NMR SOLUTION STRUCTURE ...
 
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[[Image:1ahd.gif|left|200px]]<br /><applet load="1ahd" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1ahd" />
'''DETERMINATION OF THE NMR SOLUTION STRUCTURE OF AN ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX'''<br />


==Overview==
==DETERMINATION OF THE NMR SOLUTION STRUCTURE OF AN ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX==
The nuclear magnetic resonance (NMR) solution structure of a complex, formed by the mutant Antennapedia homeodomain with Cys39 replaced by Ser, Antp(C39S), and a 14 base-pair DNA duplex containing the BS2 operator, sequence was determined using uniform 13C and 15N-labeling of the protein., Two-dimensional nuclear Overhauser enhancement spectroscopy ([1H,1H]NOESY), with 15N(omega 2)-half-filter and 13C(omega 1, omega, 2)-double-half-filter, and three-dimensional heteronuclear-correlated, [1H,1H]NOESY yielded a total of 855 intramolecular NOE upper distance, constraints in the homeodomain, 151 upper distance constraints within the, DNA duplex, and 39 intermolecular protein-DNA upper distance constraints., These data were used as the input for the structure calculation with, simulated annealing followed by molecular dynamics in a water bath and, energy refinement. A group of 16 conformers was thus generated which, represent the solution structure of the Antp(C39S) homeodomain-DNA, complex. The new structure determination confirms the salient features, reported previously from a preliminary investigation of the same complex, in particular the location of the recognition helix in the major groove, with the turn of the helix-turn-helix motif outside the contact area with, the DNA, and the N-terminal arm of the homeodomain contacting the minor, groove of the DNA. In addition, distinct amino acid side-chain-DNA, contacts could be identified, and evidence was found that the invariant, residue Asn51 (and possibly also Gln50) is in a slow dynamic equilibrium, between two or several different DNA contact sites. The molecular dynamics, calculations in a water bath yielded structures with hydration water, molecules in the protein-DNA interface, which coincides with direct NMR, observations of hydration waters. In the Appendix the experimental data, obtained with the Antp(C39S) homeodomain-DNA complex and the techniques, used for the structure calculation are evaluated using a simulated input, data set derived from the X-ray crystal structure of a DNA complex with a, homologous homeodomain. This study indicates that a nearly complete set of, NOE upper distance constraints for the Antp(C39S) homeodomain and the, protein-DNA interface was presently obtained. It further shows that the, structure calculation used here yields a precise reproduction of the, crystal structure from the simulated input data, and also results in, hydration of the protein-DNA interface in the recalculated complex.
<StructureSection load='1ahd' size='340' side='right'caption='[[1ahd]]' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1ahd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_subobscura Drosophila subobscura]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AHD FirstGlance]. <br>
1AHD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1AHD OCA].
</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=1ahd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ahd OCA], [https://pdbe.org/1ahd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ahd RCSB], [https://www.ebi.ac.uk/pdbsum/1ahd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ahd ProSAT]</span></td></tr>
==Reference==
</table>
Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex., Billeter M, Qian YQ, Otting G, Muller M, Gehring W, Wuthrich K, J Mol Biol. 1993 Dec 20;234(4):1084-93. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7903398 7903398]
== Function ==
[[Category: Drosophila melanogaster]]
[https://www.uniprot.org/uniprot/ANTP_DROSU ANTP_DROSU] Sequence-specific transcription factor which is part of a developmental regulatory system that regulates segmental identity in the mesothorax. Provides cells with specific positional identities on the anterior-posterior axis (By similarity).[UniProtKB:P02833]
[[Category: Single protein]]
== Evolutionary Conservation ==
[[Category: Billeter, M.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Gehring, W.J.]]
Check<jmol>
[[Category: Muller, M.]]
  <jmolCheckbox>
[[Category: Otting, G.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ah/1ahd_consurf.spt"</scriptWhenChecked>
[[Category: Qian, Y.Q.]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: Wuthrich, K.]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: dna binding protein/dna]]
  </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=1ahd ConSurf].
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 10:51:16 2007''
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Drosophila subobscura]]
[[Category: Large Structures]]
[[Category: Billeter M]]
[[Category: Gehring WJ]]
[[Category: Muller M]]
[[Category: Otting G]]
[[Category: Qian YQ]]
[[Category: Wuthrich K]]

Latest revision as of 15:24, 13 March 2024

DETERMINATION OF THE NMR SOLUTION STRUCTURE OF AN ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX

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