1drg: Difference between revisions

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 ==CRYSTAL STRUCTURE OF TRIMERIC CRE RECOMBINASE-LOX COMPLEX==
-<StructureSection load='1drg' size='340' side='right' caption='[[1drg]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
+<StructureSection load='1drg' size='340' side='right'caption='[[1drg]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1drg]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpp1 Bpp1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DRG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DRG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1drg]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_P1 Escherichia virus P1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DRG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DRG FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1crx|1crx]], [[2crx|2crx]], [[3crx|3crx]], [[4crx|4crx]], [[5crx|5crx]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.55&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1drg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1drg OCA], [http://pdbe.org/1drg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1drg RCSB], [http://www.ebi.ac.uk/pdbsum/1drg PDBsum]</span></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=1drg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1drg OCA], [https://pdbe.org/1drg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1drg RCSB], [https://www.ebi.ac.uk/pdbsum/1drg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1drg ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RECR_BPP1 RECR_BPP1]] Catalyzes site-specific recombination between two 34-base-pair LOXP sites. Its role is to maintain the phage genome as a monomeric unit-copy plasmid in the lysogenic state.
+[https://www.uniprot.org/uniprot/RECR_BPP1 RECR_BPP1] Catalyzes site-specific recombination between two 34-base-pair LOXP sites. Its role is to maintain the phage genome as a monomeric unit-copy plasmid in the lysogenic state.
 == 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/dr/1drg_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dr/1drg_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1drg ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The crystal structure of a novel Cre-Lox synapse was solved using phases from multiple isomorphous replacement and anomalous scattering, and refined to 2.05 A resolution. In this complex, a symmetric protein trimer is bound to a Y-shaped three-way DNA junction, a marked departure from the pseudo-4-fold symmetrical tetramer associated with Cre-mediated LoxP recombination. The three-way DNA junction was accommodated by a simple kink without significant distortion of the adjoining DNA duplexes. Although the mean angle between DNA arms in the Y and X structures was similar, adjacent Cre trimer subunits rotated 29 degrees relative to those in the tetramers. This rotation was accommodated at the protein-protein and DNA-DNA interfaces by interactions that are "quasi-equivalent" to those in the tetramer, analogous to packing differences of chemically identical viral subunits at non-equivalent positions in icosahedral capsids. This structural quasi-equivalence extends to function as Cre can bind to, cleave and perform strand transfer with a three-way Lox substrate. The structure explains the dual recognition of three and four-way junctions by site-specific recombinases as being due to shared structural features between the differently branched substrates and plasticity of the protein-protein interfaces. To our knowledge, this is the first direct demonstration of quasi-equivalence in both the assembly and function of an oligomeric enzyme.
-Quasi-equivalence in site-specific recombinase structure and function: crystal structure and activity of trimeric Cre recombinase bound to a three-way Lox DNA junction.,Woods KC, Martin SS, Chu VC, Baldwin EP J Mol Biol. 2001 Oct 12;313(1):49-69. PMID:11601846<ref>PMID:11601846</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1drg" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Resolvase|Resolvase]]
+*[[Resolvase 3D structures|Resolvase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bpp1]]
+[[Category: Escherichia virus P1]]
-[[Category: Baldwin, E P]]
+[[Category: Large Structures]]
-[[Category: Woods, K C]]
+[[Category: Baldwin EP]]
-[[Category: Branched dna]]
+[[Category: Woods KC]]
-[[Category: Hydrolase]]
-[[Category: Ligase-dna complex]]
-[[Category: Protein-dna complex]]
-[[Category: Recombination]]
-[[Category: Site-specific recombinase]]
-[[Category: Three- way junction]]
-[[Category: Trimeric]]