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==Crystal structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription== | ==Crystal structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription== | ||
<StructureSection load='6bog' size='340' side='right' caption='[[6bog]], [[Resolution|resolution]] 3.21Å' scene=''> | <StructureSection load='6bog' size='340' side='right'caption='[[6bog]], [[Resolution|resolution]] 3.21Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6bog]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3dmq 3dmq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BOG OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6bog]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_S88 Escherichia coli S88]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3dmq 3dmq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BOG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BOG FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.205Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6bog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bog OCA], [https://pdbe.org/6bog PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bog RCSB], [https://www.ebi.ac.uk/pdbsum/6bog PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bog ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/RAPA_ECO45 RAPA_ECO45] 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. | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6bog" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Helicase 3D structures|Helicase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Escherichia coli S88]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Gan J]] | ||
[[Category: | [[Category: Ji X]] | ||
[[Category: | [[Category: Jin DJ]] | ||
[[Category: | [[Category: Joachimiak A]] | ||
[[Category: | [[Category: Shaw GX]] | ||
[[Category: | [[Category: Zhang R]] | ||
[[Category: | [[Category: Zhou YN]] | ||
Latest revision as of 16:11, 30 August 2023
Crystal structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcriptionCrystal structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription
Structural highlights
FunctionRAPA_ECO45 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. Publication Abstract from PubMedRapA, 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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