2bnw: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2bnw.png|left|200px]]
-<!--
+==Structural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to direct DNA heptad repeats==
-The line below this paragraph, containing "STRUCTURE_2bnw", creates the "Structure Box" on the page.
+<StructureSection load='2bnw' size='340' side='right'caption='[[2bnw]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2bnw]] 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=2BNW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BNW FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.45&#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=2bnw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bnw OCA], [https://pdbe.org/2bnw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bnw RCSB], [https://www.ebi.ac.uk/pdbsum/2bnw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bnw ProSAT]</span></td></tr>
-{{STRUCTURE_2bnw|  PDB=2bnw  |  SCENE=  }}
+</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.
-===STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX OMEGA REPRESSOR TO DIRECT DNA HEPTAD REPEATS===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16528102}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2bnw" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16528102 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16528102}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[2bnw]] is a 8 chain structure with 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=2BNW OCA].
-==Reference==
-<ref group="xtra">PMID:016528102</ref><references group="xtra"/>
 [[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: Dna heptad]]
-[[Category: Dna-binding regulatory protein]]
-[[Category: Dna-binding-regulatory protein complex]]
-[[Category: Inc18 family]]
-[[Category: Inverted repeat]]
-[[Category: Metj/arc superfamily]]
-[[Category: Rhh]]
-[[Category: Ribbon-helix-helix]]