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| - | | + | #REDIRECT [[6bog]] This PDB entry is obsolete and replaced by 6bog |
| - | ==Crystal structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription==
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| - | <StructureSection load='3dmq' size='340' side='right' caption='[[3dmq]], [[Resolution|resolution]] 3.20Å' scene=''>
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| - | == Structural highlights ==
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| - | <table><tr><td colspan='2'>[[3dmq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DMQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DMQ FirstGlance]. <br>
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| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rapA, hepA, yabA, b0059, JW0058 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
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| - | <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=3dmq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dmq OCA], [http://pdbe.org/3dmq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dmq RCSB], [http://www.ebi.ac.uk/pdbsum/3dmq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dmq ProSAT]</span></td></tr>
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| - | </table>
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| - | == Function ==
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| - | [[http://www.uniprot.org/uniprot/RAPA_ECOLI RAPA_ECOLI]] Transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA. Does not activate transcription on linear DNA. Probably not involved in DNA repair (By similarity).<ref>PMID:11751638</ref>
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| - | == Evolutionary Conservation ==
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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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| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dm/3dmq_consurf.spt"</scriptWhenChecked>
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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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| - | </jmolCheckbox>
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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=3dmq ConSurf].
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| - | <div style="clear:both"></div>
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| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | RapA, as abundant as sigma70 in the cell, is an RNA polymerase (RNAP)-associated Swi2/Snf2 protein with ATPase activity. It stimulates RNAP recycling during transcription. We report a structure of RapA that is also a full-length structure for the entire Swi2/Snf2 family. RapA contains seven domains, two of which exhibit novel protein folds. Our model of RapA in complex with ATP and double-stranded DNA (dsDNA) suggests that RapA may bind to and translocate on dsDNA. Our kinetic template-switching assay shows that RapA facilitates the release of sequestered RNAP from a posttranscrption/posttermination complex for transcription reinitiation. Our in vitro competition experiment indicates that RapA binds to core RNAP only but is readily displaceable by sigma70. RapA is likely another general transcription factor, the structure of which provides a framework for future studies of this bacterial Swi2/Snf2 protein and its important roles in RNAP recycling during transcription.
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| - | Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription.,Shaw G, Gan J, Zhou YN, Zhi H, Subburaman P, Zhang R, Joachimiak A, Jin DJ, Ji X Structure. 2008 Sep 10;16(9):1417-27. PMID:18786404<ref>PMID:18786404</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 3dmq" style="background-color:#fffaf0;"></div>
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| - | ==See Also==
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| - | *[[Helicase|Helicase]]
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| - | *[[RapA%2C a Swi2/Snf2 protein|RapA%2C a Swi2/Snf2 protein]]
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| - | == References ==
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| - | <references/>
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| - | __TOC__
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| - | </StructureSection>
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| - | [[Category: Ecoli]]
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| - | [[Category: Gan, J]]
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| - | [[Category: Ji, X]]
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| - | [[Category: Jin, D J]]
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| - | [[Category: Joachimiak, A]]
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| - | [[Category: Shaw, G]]
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| - | [[Category: Zhang, R]]
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| - | [[Category: Zhou, Y N]]
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| - | [[Category: Activator]]
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| - | [[Category: Atp-binding]]
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| - | [[Category: Dna-binding]]
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| - | [[Category: Helicase]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: Nucleotide-binding]]
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| - | [[Category: Rapa]]
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| - | [[Category: Rna polymerase recycling]]
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| - | [[Category: Swf2/snf2]]
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| - | [[Category: Transcription factor]]
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| - | [[Category: Transcription regulation]]
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