2p4v: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
 
Line 3: Line 3:
<StructureSection load='2p4v' size='340' side='right'caption='[[2p4v]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
<StructureSection load='2p4v' size='340' side='right'caption='[[2p4v]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2p4v]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P4V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P4V FirstGlance]. <br>
<table><tr><td colspan='2'>[[2p4v]] is a 6 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=2P4V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P4V FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1grj|1grj]], [[2eul|2eul]], [[2etn|2etn]], [[2f23|2f23]]</div></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]] 2.6&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">greB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2p4v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p4v OCA], [https://pdbe.org/2p4v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p4v RCSB], [https://www.ebi.ac.uk/pdbsum/2p4v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p4v 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=2p4v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p4v OCA], [https://pdbe.org/2p4v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p4v RCSB], [https://www.ebi.ac.uk/pdbsum/2p4v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p4v ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/GREB_ECOL6 GREB_ECOL6]] Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus. GreB releases sequences of up to 9 nucleotides in length (By similarity).  
[https://www.uniprot.org/uniprot/GREB_ECOLI GREB_ECOLI] Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus. GreB releases sequences of up to 9 nucleotides in length.[HAMAP-Rule:MF_00930]<ref>PMID:8431948</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 20: Line 19:
</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=2p4v ConSurf].
</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=2p4v ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Bacterial Gre transcript cleavage factors stimulate the intrinsic endonucleolytic activity of RNA polymerase (RNAP) to rescue stalled transcription complexes. They bind to RNAP and extend their coiled-coil (CC) domains to the catalytic centre through the secondary channel. Three existing models for the Gre-RNAP complex postulate congruent mechanisms of Gre-assisted catalysis, while offering conflicting views of the Gre-RNAP interactions. Here, we report the GreB structure of Escherichia coli. The GreB monomers form a triangle with the tip of the amino-terminal CC of one molecule trapped within the hydrophobic cavity of the carboxy-terminal domain of a second molecule. This arrangement suggests an analogous model for recruitment to RNAP. Indeed, the beta'-subunit CC located at the rim of the secondary channel has conserved hydrophobic residues at its tip. We show that substitutions of these residues and those in the GreB C-terminal domain cavity confer defects in GreB activity and binding to RNAP, and present a plausible model for the RNAP-GreB complex.
The carboxy-terminal coiled-coil of the RNA polymerase beta'-subunit is the main binding site for Gre factors.,Vassylyeva MN, Svetlov V, Dearborn AD, Klyuyev S, Artsimovitch I, Vassylyev DG EMBO Rep. 2007 Nov;8(11):1038-43. Epub 2007 Oct 5. PMID:17917675<ref>PMID:17917675</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2p4v" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
Line 36: Line 26:
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus coli migula 1895]]
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Artsimovitch, I]]
[[Category: Artsimovitch I]]
[[Category: Dearborn, A D]]
[[Category: Dearborn AD]]
[[Category: Klyuyev, S]]
[[Category: Klyuyev S]]
[[Category: Svetlov, V]]
[[Category: Svetlov V]]
[[Category: Vassylyev, D G]]
[[Category: Vassylyev DG]]
[[Category: Vassylyeva, M N]]
[[Category: Vassylyeva MN]]
[[Category: Gre-factor]]
[[Category: Rna polymerase]]
[[Category: Transcript cleavage]]
[[Category: Transcription]]
Retrieved from "https://proteopedia.org/2p4v"