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New page: left|200px<br /><applet load="2cax" size="350" color="white" frame="true" align="right" spinBox="true" caption="2cax, resolution 2.90Å" /> '''STRUCTURAL BASIS FOR...
 
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[[Image:2cax.gif|left|200px]]<br /><applet load="2cax" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2cax, resolution 2.90&Aring;" />
'''STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX REPRESSOR OMEGA TO MUTATED DIRECT DNA HEPTAD REPEATS'''<br />


==Overview==
==STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX REPRESSOR OMEGA TO MUTATED DIRECT DNA HEPTAD REPEATS==
Repressor omega regulates transcription of genes required for copy number, control, accurate segregation and stable maintenance of inc18 plasmids, hosted by Gram-positive bacteria. omega belongs to homodimeric, ribbon-helix-helix (RHH2) repressors typified by a central, antiparallel, beta-sheet for DNA major groove binding. Homodimeric omega2 binds, cooperatively to promotors with 7 to 10 consecutive non-palindromic DNA, heptad repeats (5'-(A)/(T)ATCAC(A)/(T)-3', symbolized by --&gt;) in, palindromic inverted, converging (--&gt;&lt;--) or diverging (&lt;----&gt;), orientation and also, unique to omega2 and contrasting other RHH2, repressors, to non-palindromic direct (--&gt;--&gt;) repeats. Here we, investigate with crystal structures how omega2 binds specifically to, heptads in minimal operators with (--&gt;--&gt;) and (--&gt;&lt;--) repeats. Since the, pseudo-2-fold axis relating the monomers in omega(2) passes the central, C-G base pair of each heptad with approximately 0.3 A downstream offset, the separation between the pseudo-2-fold axes is exactly 7 bp in (--&gt;--&gt;), approximately 0.6 A shorter in (--&gt;&lt;--) but would be approximately 0.6 A, longer in (&lt;----&gt;). These variations grade interactions between adjacent, omega2 and explain modulations in cooperative binding affinity of omega2, to operators with different heptad orientations.
<StructureSection load='2cax' size='340' side='right'caption='[[2cax]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2cax]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pyogenes Streptococcus pyogenes] 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=2CAX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CAX FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#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=2cax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cax OCA], [https://pdbe.org/2cax PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cax RCSB], [https://www.ebi.ac.uk/pdbsum/2cax PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cax ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q57468_STRPY Q57468_STRPY]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Repressor omega regulates transcription of genes required for copy number control, accurate segregation and stable maintenance of inc18 plasmids hosted by Gram-positive bacteria. omega belongs to homodimeric ribbon-helix-helix (RHH2) repressors typified by a central, antiparallel beta-sheet for DNA major groove binding. Homodimeric omega2 binds cooperatively to promotors with 7 to 10 consecutive non-palindromic DNA heptad repeats (5'-(A)/(T)ATCAC(A)/(T)-3', symbolized by --&gt;) in palindromic inverted, converging (--&gt;&lt;--) or diverging (&lt;----&gt;) orientation and also, unique to omega2 and contrasting other RHH2 repressors, to non-palindromic direct (--&gt;--&gt;) repeats. Here we investigate with crystal structures how omega2 binds specifically to heptads in minimal operators with (--&gt;--&gt;) and (--&gt;&lt;--) repeats. Since the pseudo-2-fold axis relating the monomers in omega(2) passes the central C-G base pair of each heptad with approximately 0.3 A downstream offset, the separation between the pseudo-2-fold axes is exactly 7 bp in (--&gt;--&gt;), approximately 0.6 A shorter in (--&gt;&lt;--) but would be approximately 0.6 A longer in (&lt;----&gt;). These variations grade interactions between adjacent omega2 and explain modulations in cooperative binding affinity of omega2 to operators with different heptad orientations.


==About this Structure==
Structures of omega repressors bound to direct and inverted DNA repeats explain modulation of transcription.,Weihofen WA, Cicek A, Pratto F, Alonso JC, Saenger W Nucleic Acids Res. 2006 Mar 9;34(5):1450-8. Print 2006. PMID:16528102<ref>PMID:16528102</ref>
2CAX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_pyogenes Streptococcus pyogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CAX OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Structures of omega repressors bound to direct and inverted DNA repeats explain modulation of transcription., Weihofen WA, Cicek A, Pratto F, Alonso JC, Saenger W, Nucleic Acids Res. 2006 Mar 9;34(5):1450-8. Print 2006. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16528102 16528102]
</div>
[[Category: Single protein]]
<div class="pdbe-citations 2cax" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Streptococcus pyogenes]]
[[Category: Streptococcus pyogenes]]
[[Category: Alonso, J.C.]]
[[Category: Synthetic construct]]
[[Category: Cicek, A.]]
[[Category: Alonso JC]]
[[Category: Pratto, F.]]
[[Category: Cicek A]]
[[Category: Saenger, W.]]
[[Category: Pratto F]]
[[Category: Weihofen, W.A.]]
[[Category: Saenger W]]
[[Category: cooperative dna binding]]
[[Category: Weihofen WA]]
[[Category: direct repeats]]
[[Category: dna heptad 5'-a/t atcac a/t -3']]
[[Category: dna-binding]]
[[Category: inc18 family]]
[[Category: inc18 family of plasmids]]
[[Category: inverted repeats]]
[[Category: metj/arc superfamily]]
[[Category: plasmid maintenance]]
[[Category: regulatory protein]]
[[Category: rhh]]
[[Category: ribbon-helix-helix]]
[[Category: transcriptional repressor]]
 
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