2vum: Difference between revisions
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[[Image: | ==Alpha-amanitin inhibited complete RNA polymerase II elongation complex== | ||
<StructureSection load='2vum' size='340' side='right' caption='[[2vum]], [[Resolution|resolution]] 3.40Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2vum]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Amanita_phalloides Amanita phalloides] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VUM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VUM FirstGlance]. <br> | |||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br> | |||
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene>, <scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=ILX:4,5-DIHYDROXYISOLEUCINE'>ILX</scene>, <scene name='pdbligand=TRX:6-HYDROXYTRYPTOPHAN'>TRX</scene></td></tr> | |||
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1k83|1k83]], [[3cqz|3cqz]], [[1twc|1twc]], [[1i6h|1i6h]], [[1y1v|1y1v]], [[1y77|1y77]], [[1y1y|1y1y]], [[1wcm|1wcm]], [[1r9s|1r9s]], [[1twg|1twg]], [[1sfo|1sfo]], [[1i50|1i50]], [[1twa|1twa]], [[1r5u|1r5u]], [[1nik|1nik]], [[1twh|1twh]], [[1r9t|1r9t]], [[2ja7|2ja7]], [[2ja6|2ja6]], [[1a1d|1a1d]], [[1dzf|1dzf]], [[1y14|1y14]], [[1y1w|1y1w]], [[1nt9|1nt9]], [[2b63|2b63]], [[1twf|1twf]], [[1i3q|1i3q]], [[1pqv|1pqv]], [[2b8k|2b8k]], [[2ja8|2ja8]], [[2ja5|2ja5]]</td></tr> | |||
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr> | |||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vum OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vum RCSB], [http://www.ebi.ac.uk/pdbsum/2vum PDBsum]</span></td></tr> | |||
<table> | |||
== 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/vu/2vum_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/chain_selection.php?pdb_ID=2ata ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
To study how RNA polymerase II translocates after nucleotide incorporation, we prepared elongation complex crystals in which pre- and post-translocation states interconvert. Crystal soaking with the inhibitor alpha-amanitin locked the elongation complex in a new state, which was refined at 3.4-A resolution and identified as a possible translocation intermediate. The DNA base entering the active site occupies a 'pretemplating' position above the central bridge helix, which is shifted and occludes the templating position. A leucine residue in the trigger loop forms a wedge at the shifted bridge helix, but moves by 13 A to close the active site during nucleotide incorporation. Our results support a Brownian ratchet mechanism that involves swinging of the trigger loop between open, wedged and closed positions, and suggest that alpha-amanitin impairs nucleotide incorporation and translocation by trapping the trigger loop and bridge helix. | |||
Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation.,Brueckner F, Cramer P Nat Struct Mol Biol. 2008 Aug;15(8):811-8. Epub 2008 Jun 13. PMID:18552824<ref>PMID:18552824</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
==See Also== | ==See Also== | ||
*[[RNA polymerase|RNA polymerase]] | *[[RNA polymerase|RNA polymerase]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Amanita phalloides]] | [[Category: Amanita phalloides]] | ||
[[Category: DNA-directed RNA polymerase]] | [[Category: DNA-directed RNA polymerase]] | ||
Revision as of 09:17, 29 September 2014
Alpha-amanitin inhibited complete RNA polymerase II elongation complex
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