1r71

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[[Image:1r71.gif|left|200px]]
 
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{{Structure
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==Crystal Structure of the DNA binding domain of KorB in complex with the operator DNA==
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|PDB= 1r71 |SIZE=350|CAPTION= <scene name='initialview01'>1r71</scene>, resolution 2.20&Aring;
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<StructureSection load='1r71' size='340' side='right'caption='[[1r71]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=BRU:5-BROMO-2&#39;-DEOXYURIDINE-5&#39;-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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<table><tr><td colspan='2'>[[1r71]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R71 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R71 FirstGlance]. <br>
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|ACTIVITY=
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</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>
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|GENE= KORB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1r71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r71 OCA], [https://pdbe.org/1r71 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r71 RCSB], [https://www.ebi.ac.uk/pdbsum/1r71 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r71 ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1r71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r71 OCA], [http://www.ebi.ac.uk/pdbsum/1r71 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1r71 RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/KORB2_ECOLX KORB2_ECOLX] In conjunction with KorA, inhibits the transcription of the kilA, trfA and korAB operons. Is also involved in the negative control of the kilB operon.
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== Evolutionary Conservation ==
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'''Crystal Structure of the DNA binding domain of KorB in complex with the operator DNA'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r7/1r71_consurf.spt"</scriptWhenChecked>
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The KorB protein of the broad-host-range plasmid RP4 acts as a multifunctional regulator of plasmid housekeeping genes, including those responsible for replication, maintenance and conjugation. Additionally, KorB functions as the ParB analog of the plasmid's partitioning system. The protein structure consists of eight helices, two of which belong to a predicted helix-turn-helix motif. Each half-site of the palindromic operator DNA binds one copy of the protein in the major groove. As confirmed by mutagenesis, recognition specificity is based mainly on two side chain interactions outside the helix-turn-helix motif with two bases next to the central base pair of the 13-base pair operator sequence. The surface of the KorB DNA-binding domain mirrors the overall acidity of KorB, whereas DNA binding occurs via a basic interaction surface. We present a model of KorB, including the structure of its dimerization domain, and discuss its interactions with the highly basic ParA homolog IncC.
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==About this Structure==
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</jmolCheckbox>
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1R71 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R71 OCA].
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</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=1r71 ConSurf].
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<div style="clear:both"></div>
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==Reference==
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__TOC__
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Sequence-specific DNA binding determined by contacts outside the helix-turn-helix motif of the ParB homolog KorB., Khare D, Ziegelin G, Lanka E, Heinemann U, Nat Struct Mol Biol. 2004 Jul;11(7):656-63. Epub 2004 May 30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15170177 15170177]
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Heinemann, U.]]
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[[Category: Heinemann U]]
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[[Category: Khare, D.]]
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[[Category: Khare D]]
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[[Category: Lanka, E.]]
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[[Category: Lanka E]]
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[[Category: Ziegelin, G.]]
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[[Category: Ziegelin G]]
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[[Category: heilx-turn-helix motif]]
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[[Category: incp]]
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[[Category: parb homologue]]
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[[Category: plasmid partitioning]]
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[[Category: protein-dna complex]]
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[[Category: transcription factor]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:24:08 2008''
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Current revision

Crystal Structure of the DNA binding domain of KorB in complex with the operator DNA

PDB ID 1r71

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OCA

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