View source for 1kbu


==CRE RECOMBINASE BOUND TO A LOXP HOLLIDAY JUNCTION==
<StructureSection load='1kbu' size='340' side='right'caption='[[1kbu]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1kbu]] 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=1KBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KBU 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]] 2.2&#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=1kbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kbu OCA], [https://pdbe.org/1kbu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kbu RCSB], [https://www.ebi.ac.uk/pdbsum/1kbu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kbu 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/kb/1kbu_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=1kbu ConSurf].
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== Publication Abstract from PubMed ==
Cre recombinase uses two pairs of sequential cleavage and religation reactions to exchange homologous DNA strands between 34 base-pair (bp) LoxP recognition sequences. In the oligomeric recombination complex, a switch between "cleaving" and "non-cleaving" subunit conformations regulates the number, order, and regio-specificity of the strand exchanges. However, the particular sequence of events has been in question. From analysis of strand composition of the Holliday junction (HJ) intermediate, we determined that Cre initiates recombination of LoxP by cleaving the upper strand on the left arm. Cre preferred to react with the left arm of a LoxP suicide substrate, but at a similar rate to the right arm, indicating that the first strand to be exchanged is selected prior to cleavage. We propose that during complex assembly the cleaving subunit preferentially associates with the LoxP left arm, directing the first strand exchange to that side. In addition, this biased assembly would enforce productive orientation of LoxP sites in the recombination synapses. A novel Cre-HJ complex structure in which LoxP was oriented with the left arm bound by the cleaving Cre subunit suggested a physical basis for the strand exchange order. Lys86 and Lys201 interact with the left arm scissile adenine base differently than in structures that have a scissile guanine. These interactions are associated with positioning the 198-208 loop, a structural component of the conformational switch, in a configuration that is specific to the cleaving conformation. Our results suggest that strand exchange order and site alignment are regulated by an "induced fit" mechanism in which the cleaving conformation is selectively stabilized through protein-DNA interactions with the scissile base on the strand that is cleaved first.

The order of strand exchanges in Cre-LoxP recombination and its basis suggested by the crystal structure of a Cre-LoxP Holliday junction complex.,Martin SS, Pulido E, Chu VC, Lechner TS, Baldwin EP J Mol Biol. 2002 May 24;319(1):107-27. PMID:12051940<ref>PMID:12051940</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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==See Also==
*[[Resolvase 3D structures|Resolvase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia virus P1]]
[[Category: Large Structures]]
[[Category: Baldwin EP]]
[[Category: Chu VC]]
[[Category: Lechner T]]
[[Category: Martin SS]]
[[Category: Pulido E]]