2ovg: Difference between revisions

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-[[Image:2ovg.jpg|left|200px]]<br /><applet load="2ovg" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2ovg, resolution 1.350&Aring;" />
-'''Lambda Cro Q27P/A29S/K32Q triple mutant at 1.35 A in space group P3221'''<br />
-==Overview==
+==Lambda Cro Q27P/A29S/K32Q triple mutant at 1.35 A in space group P3221==
-Previously reported crystal structures of free and DNA-bound dimers of, lambda Cro differ strongly (about 4 A backbone rmsd), suggesting both, flexibility of the dimer interface and induced-fit protein structure, changes caused by sequence-specific DNA binding. Here, we present two, crystal structures, in space groups P3(2)21 and C2 at 1.35 and 1.40 A, resolution, respectively, of a variant of lambda Cro with three mutations, in its recognition helix (Q27P/A29S/K32Q, or PSQ for short). One dimer, structure (P3(2)21; PSQ form 1) resembles the DNA-bound wild-type Cro, dimer (1.0 A backbone rmsd), while the other (C2; PSQ form 2) resembles, neither unbound (3.6 A) nor bound (2.4 A) wild-type Cro. Both PSQ form 2, and unbound wild-type dimer crystals have a similar interdimer beta-sheet, interaction between the beta1 strands at the edges of the dimer. In the, former, an infinite, open beta-structure along one crystal axis results, while in the latter, a closed tetrameric barrel is formed. Neither the, DNA-bound wild-type structure nor PSQ form 1 contains these interdimer, interactions. We propose that beta-sheet superstructures resulting from, crystal contact interactions distort Cro dimers from their preferred, solution conformation, which actually resembles the DNA-bound structure., These results highlight the remarkable flexibility of lambda Cro but also, suggest that sequence-specific DNA binding may not induce large changes in, the protein structure.
+<StructureSection load='2ovg' size='340' side='right'caption='[[2ovg]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2ovg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Lambda Escherichia virus Lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OVG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OVG 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]] 1.35&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=2ovg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ovg OCA], [https://pdbe.org/2ovg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ovg RCSB], [https://www.ebi.ac.uk/pdbsum/2ovg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ovg ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RCRO_LAMBD RCRO_LAMBD] Cro represses genes normally expressed in early phage development and is necessary for the late stage of lytic growth. It does this by binding to the OL and OR operators regions normally used by the repressor protein for lysogenic maintenance.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ov/2ovg_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </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=2ovg ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Previously reported crystal structures of free and DNA-bound dimers of lambda Cro differ strongly (about 4 A backbone rmsd), suggesting both flexibility of the dimer interface and induced-fit protein structure changes caused by sequence-specific DNA binding. Here, we present two crystal structures, in space groups P3(2)21 and C2 at 1.35 and 1.40 A resolution, respectively, of a variant of lambda Cro with three mutations in its recognition helix (Q27P/A29S/K32Q, or PSQ for short). One dimer structure (P3(2)21; PSQ form 1) resembles the DNA-bound wild-type Cro dimer (1.0 A backbone rmsd), while the other (C2; PSQ form 2) resembles neither unbound (3.6 A) nor bound (2.4 A) wild-type Cro. Both PSQ form 2 and unbound wild-type dimer crystals have a similar interdimer beta-sheet interaction between the beta1 strands at the edges of the dimer. In the former, an infinite, open beta-structure along one crystal axis results, while in the latter, a closed tetrameric barrel is formed. Neither the DNA-bound wild-type structure nor PSQ form 1 contains these interdimer interactions. We propose that beta-sheet superstructures resulting from crystal contact interactions distort Cro dimers from their preferred solution conformation, which actually resembles the DNA-bound structure. These results highlight the remarkable flexibility of lambda Cro but also suggest that sequence-specific DNA binding may not induce large changes in the protein structure.
-==About this Structure==
+Two structures of a lambda Cro variant highlight dimer flexibility but disfavor major dimer distortions upon specific binding of cognate DNA.,Hall BM, Roberts SA, Heroux A, Cordes MH J Mol Biol. 2008 Jan 18;375(3):802-11. Epub 2007 Nov 6. PMID:18054042<ref>PMID:18054042</ref>
-OVG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=EPE:'>EPE</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OVG OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Two structures of a lambda Cro variant highlight dimer flexibility but disfavor major dimer distortions upon specific binding of cognate DNA., Hall BM, Roberts SA, Heroux A, Cordes MH, J Mol Biol. 2008 Jan 18;375(3):802-11. Epub 2007 Nov 6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18054042 18054042]
+</div>
-[[Category: Enterobacteria phage lambda]]
+<div class="pdbe-citations 2ovg" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
+== References ==
-[[Category: Cordes, M.H.]]
+<references/>
-[[Category: Hall, B.M.]]
+__TOC__
-[[Category: Heroux, A.]]
+</StructureSection>
-[[Category: Horton, N.C.]]
+[[Category: Escherichia virus Lambda]]
-[[Category: Roberts, S.A.]]
+[[Category: Large Structures]]
-[[Category: EPE]]
+[[Category: Cordes MH]]
-[[Category: SO4]]
+[[Category: Hall BM]]
-[[Category: bacteriophage]]
+[[Category: Heroux A]]
-[[Category: flexibility]]
+[[Category: Roberts SA]]
-[[Category: helix-turn-helix]]
-[[Category: transcription factor]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb  6 15:31:40 2008''