View source for 3jxd


==Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9C in the presence of Rb+==
<StructureSection load='3jxd' size='340' side='right'caption='[[3jxd]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3jxd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_virus_P22 Salmonella virus P22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JXD 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]] 2.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></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=3jxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jxd OCA], [https://pdbe.org/3jxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jxd RCSB], [https://www.ebi.ac.uk/pdbsum/3jxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jxd ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RPC2_BPP22 RPC2_BPP22] This protein allows the phage to reside inactively in the chromosome of its host bacterium. This lysogenic state is maintained by binding of regulatory protein C2 to the OR and OL operators, preventing transcription of proteins necessary for lytic development.
== 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/jx/3jxd_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=3jxd ConSurf].
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== Publication Abstract from PubMed ==
The binding of proteins to specific sequences of DNA is an important feature of virtually all DNA transactions. Proteins recognize specific DNA sequences using both direct readout (sensing types and positions of DNA functional groups) and indirect readout (sensing DNA conformation and deformability). Previously we showed that the P22 c2 repressor N-terminal domain (P22R NTD) forces the central non-contacted 5'-ATAT-3' sequence of the DNA operator into the B' state, a state known to affect DNA hydration, rigidity and bending. Usually the B' state, with a narrow minor groove and a spine of hydration, is reserved for A-tract DNA (TpA steps disrupt A-tracts). Here, we have co-crystallized P22R NTD with an operator containing a central 5'-ACGT-3' sequence in the non-contacted region. C.G base pairs have not previously been observed in the B' state and are thought to prevent it. However, P22R NTD induces a narrow minor groove and a spine of hydration to 5'-ACGT-3'. We observe that C.G base pairs have distinctive destabilizing and disordering effects on the spine of hydration. It appears that the reduced stability of the spine results in a higher energy cost for the B to B' transition. The differential effect of DNA sequence on the barrier to this transition allows the protein to sense the non-contacted DNA sequence.

Sequence recognition of DNA by protein-induced conformational transitions.,Watkins D, Mohan S, Koudelka GB, Williams LD J Mol Biol. 2010 Mar 5;396(4):1145-64. Epub 2010 Jan 4. PMID:20053356<ref>PMID:20053356</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 3jxd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Salmonella virus P22]]
[[Category: Koudelka GB]]
[[Category: Watkins D]]
[[Category: Williams LD]]