1ma7: Difference between revisions

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-[[Image:1ma7.gif|left|200px]]<br /><applet load="1ma7" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1ma7, resolution 2.3&Aring;" />
-'''Crystal structure of Cre site-specific recombinase complexed with a mutant DNA substrate, LoxP-A8/T27'''<br />
-==Overview==
+==Crystal structure of Cre site-specific recombinase complexed with a mutant DNA substrate, LoxP-A8/T27==
-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.
+<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 [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='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'>[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 ==
+[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>
+    <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=1ma7 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-MA7 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_p21 Enterobacteria phage p21]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1MA7 OCA].
+*[[Resolvase 3D structures|Resolvase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12779336 12779336]
+[[Category: Escherichia virus P1]]
-[[Category: Enterobacteria phage p21]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Baldwin EP]]
-[[Category: Baldwin, E.P.]]
+[[Category: Chu VC]]
-[[Category: Chu, V.C.]]
+[[Category: Martin SS]]
-[[Category: Martin, S.S.]]
-[[Category: cre-lox site-specific recombination]]
-[[Category: protein-dna complex]]
-[[Category: specificity of protein-dna interactions]]
-[[Category: tyrosine recombinase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:16:10 2007''