1ma7: Difference between revisions

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 ==Crystal structure of Cre site-specific recombinase complexed with a mutant DNA substrate, LoxP-A8/T27==
-<StructureSection load='1ma7' size='340' side='right' caption='[[1ma7]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='1ma7' size='340' side='right'caption='[[1ma7]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ma7]] is a 4 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=1MA7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MA7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ma7]] is a 4 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=1MA7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MA7 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kbu|1kbu]], [[1crx|1crx]], [[3crx|3crx]], [[4crx|4crx]], [[1f44|1f44]]</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]] 2.3&#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=1ma7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ma7 OCA], [http://pdbe.org/1ma7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ma7 RCSB], [http://www.ebi.ac.uk/pdbsum/1ma7 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=1ma7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ma7 OCA], [https://pdbe.org/1ma7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ma7 RCSB], [https://www.ebi.ac.uk/pdbsum/1ma7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ma7 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/ma/1ma7_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ma/1ma7_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=1ma7 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Cre promotes recombination at the 34 bp LoxP sequence. Substitution of a critical C-G base pair in LoxP with an A-T base pair, to give LoxAT, reduced Cre binding in vitro and abolished recombination in vivo [Hartung, M., and Kisters-Woike, B. (1998) J. Biol. Chem. 273, 22884-22891].We demonstrated that LoxAT can be recombined in vitro. However, Cre discriminates against this substrate both before and after DNA binding. The preference for LoxP over LoxAT is the result of reduced binding and a slower turnover rate, amplified by changes in cooperativity of complex assembly. With LoxAT, similar levels of substrate turnover required 2-2.5-fold higher protein-DNA concentrations compared to LoxP, but the sigmoidal behavior of the concentration dependence was more pronounced. Further, the Cre-LoxAT complexes reacted 4-5-fold more slowly. In the 2.3 A resolution Cre-LoxAT complex structure, the major groove Arg259-guanine interaction was disrupted, explaining the reduced binding. Overall structural shifts and mobility changes indicate more favorable interactions between subunits, providing a hypothesis for the reduced turnover rate. Concomitant with the displacement of Arg259 from the DNA, adjacent charged residues Glu262 and Glu266 shifted to form salt bridges with the Arg259 guanidinium moiety. Substitution of Glu262 and Glu266 with glutamine increased Cre complex assembly efficiency and reaction rates with both LoxAT and LoxP, but diminished Cre's ability to distinguish them. The increased rate of this variant suggests that DNA substrate binding and turnover are coupled. The improved efficiency, made at some expense of sequence discrimination, may be useful for enhancing recombination in vivo.
-Modulation of the active complex assembly and turnover rate by protein-DNA interactions in Cre-LoxP recombination.,Martin SS, Chu VC, Baldwin E Biochemistry. 2003 Jun 10;42(22):6814-26. PMID:12779336<ref>PMID:12779336</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1ma7" 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: Chu, V C]]
+[[Category: Baldwin EP]]
-[[Category: Martin, S S]]
+[[Category: Chu VC]]
-[[Category: Cre-lox site-specific recombination]]
+[[Category: Martin SS]]
-[[Category: Hydrolase]]
-[[Category: Ligase-dna complex]]
-[[Category: Protein-dna complex]]
-[[Category: Specificity of protein-dna interaction]]
-[[Category: Tyrosine recombinase]]