2cax: Difference between revisions

Revision as of 21:36, 3 May 2008

STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX REPRESSOR OMEGA TO MUTATED DIRECT DNA HEPTAD REPEATS

OverviewOverview

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 -->) in palindromic inverted, converging (--><--) or diverging (<---->) orientation and also, unique to omega2 and contrasting other RHH2 repressors, to non-palindromic direct (-->-->) repeats. Here we investigate with crystal structures how omega2 binds specifically to heptads in minimal operators with (-->-->) and (--><--) 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 (-->-->), approximately 0.6 A shorter in (--><--) but would be approximately 0.6 A longer in (<---->). These variations grade interactions between adjacent omega2 and explain modulations in cooperative binding affinity of omega2 to operators with different heptad orientations.

About this StructureAbout this Structure

2CAX is a Single protein structure of sequence from Streptococcus pyogenes. Full crystallographic information is available from OCA.

ReferenceReference

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 Page seeded by OCA on Sat May 3 21:36:26 2008

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

OCA

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 [[Image:2cax.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 2cax |SIZE=350|CAPTION= <scene name='initialview01'>2cax</scene>, resolution 2.90&Aring;
+The line below this paragraph, containing "STRUCTURE_2cax", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY=
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_2cax|  PDB=2cax  |  SCENE=  }}
-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cax OCA], [http://www.ebi.ac.uk/pdbsum/2cax PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2cax RCSB]</span>
-}}
 '''STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX REPRESSOR OMEGA TO MUTATED DIRECT DNA HEPTAD REPEATS'''
@@ Line 30: / Line 27: @@
 [[Category: Saenger, W.]]
 [[Category: Weihofen, W A.]]
-[[Category: cooperative dna binding]]
+[[Category: Cooperative dna binding]]
-[[Category: direct repeat]]
+[[Category: Direct repeat]]
-[[Category: dna heptad 5'-a/t atcac a/t -3s']]
+[[Category: Dna heptad 5'-a/t atcac a/t -3s']]
-[[Category: dna-binding]]
+[[Category: Dna-binding]]
-[[Category: inc18 family]]
+[[Category: Inc18 family]]
-[[Category: inc18 family of plasmid]]
+[[Category: Inc18 family of plasmid]]
-[[Category: inverted repeat]]
+[[Category: Inverted repeat]]
-[[Category: metj/arc superfamily]]
+[[Category: Metj/arc superfamily]]
-[[Category: plasmid maintenance]]
+[[Category: Plasmid maintenance]]
-[[Category: regulatory protein]]
+[[Category: Regulatory protein]]
-[[Category: rhh]]
+[[Category: Rhh]]
-[[Category: ribbon-helix-helix]]
+[[Category: Ribbon-helix-helix]]
-[[Category: transcriptional repressor]]
+[[Category: Transcriptional repressor]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 21:36:26 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:18:54 2008''