6p0u: Difference between revisions

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<StructureSection load='6p0u' size='340' side='right'caption='[[6p0u]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
<StructureSection load='6p0u' size='340' side='right'caption='[[6p0u]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6p0u]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_lambda Bacteriophage lambda] and [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P0U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P0U FirstGlance]. <br>
<table><tr><td colspan='2'>[[6p0u]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli], [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [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=6P0U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P0U FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">fis, b3261, JW3229 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), xis ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Bacteriophage lambda])</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]] 3.3&#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=6p0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p0u OCA], [http://pdbe.org/6p0u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p0u RCSB], [http://www.ebi.ac.uk/pdbsum/6p0u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p0u ProSAT]</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=6p0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p0u OCA], [https://pdbe.org/6p0u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p0u RCSB], [https://www.ebi.ac.uk/pdbsum/6p0u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p0u ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/VXIS_LAMBD VXIS_LAMBD]] Excisionase and integrase are necessary for the excision of prophage from the host genome by site-specific recombination at the att site. [[http://www.uniprot.org/uniprot/FIS_ECOLI FIS_ECOLI]] Activates ribosomal RNA transcription, as well other genes. Plays a direct role in upstream activation of rRNA promoters. Binds to a recombinational enhancer sequence that is required to stimulate hin-mediated DNA inversion. Prevents initiation of DNA replication from oriC.<ref>PMID:2209559</ref> <ref>PMID:8836178</ref>
[https://www.uniprot.org/uniprot/FIS_ECOLI FIS_ECOLI] Activates ribosomal RNA transcription, as well other genes. Plays a direct role in upstream activation of rRNA promoters. Binds to a recombinational enhancer sequence that is required to stimulate hin-mediated DNA inversion. Prevents initiation of DNA replication from oriC.<ref>PMID:2209559</ref> <ref>PMID:8836178</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Localized arrays of proteins cooperatively assemble onto chromosomes to control DNA activity in many contexts. Binding cooperativity is often mediated by specific protein-protein interactions, but cooperativity through DNA structure is becoming increasingly recognized as an additional mechanism. During the site-specific DNA recombination reaction that excises phage lambda from the chromosome, the bacterial DNA architectural protein Fis recruits multiple lambda-encoded Xis proteins to the attR recombination site. Here, we report X-ray crystal structures of DNA complexes containing Fis + Xis, which show little, if any, contacts between the two proteins. Comparisons with structures of DNA complexes containing only Fis or Xis, together with mutant protein and DNA binding studies, support a mechanism for cooperative protein binding solely by DNA allostery. Fis binding both molds the minor groove to potentiate insertion of the Xis beta-hairpin wing motif and bends the DNA to facilitate Xis-DNA contacts within the major groove. The Fis-structured minor groove shape that is optimized for Xis binding requires a precisely positioned pyrimidine-purine base-pair step, whose location has been shown to modulate minor groove widths in Fis-bound complexes to different DNA targets.
 
Cooperative DNA binding by proteins through DNA shape complementarity.,Hancock SP, Cascio D, Johnson RC Nucleic Acids Res. 2019 Sep 19;47(16):8874-8887. doi: 10.1093/nar/gkz642. PMID:31616952<ref>PMID:31616952</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6p0u" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacteriophage lambda]]
[[Category: Escherichia coli]]
[[Category: Ecoli]]
[[Category: Escherichia coli K-12]]
[[Category: Escherichia virus Lambda]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cascio, D]]
[[Category: Cascio D]]
[[Category: Hancock, S P]]
[[Category: Hancock SP]]
[[Category: Johnson, R C]]
[[Category: Johnson RC]]
[[Category: Cooperative binding]]
[[Category: Dna binding protein]]
[[Category: Dna binding protein-dna complex]]
[[Category: Dna shape]]
[[Category: Protein-dna ternary complex]]
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