3how

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[[Image:3how.png|left|200px]]
 
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{{STRUCTURE_3how| PDB=3how | SCENE= }}
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==Complete RNA polymerase II elongation complex III with a T-U mismatch and a frayed RNA 3'-uridine==
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<StructureSection load='3how' size='340' side='right'caption='[[3how]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3how]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HOW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HOW FirstGlance]. <br>
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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]] 3.6&#8491;</td></tr>
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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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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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=3how FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3how OCA], [https://pdbe.org/3how PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3how RCSB], [https://www.ebi.ac.uk/pdbsum/3how PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3how ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RPAB2_YEAST RPAB2_YEAST] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds (By similarity).
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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/ho/3how_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3how 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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We show that RNA polymerase (Pol) II prevents erroneous transcription in vitro with different strategies that depend on the type of DNARNA base mismatch. Certain mismatches are efficiently formed but impair RNA extension. Other mismatches allow for RNA extension but are inefficiently formed and efficiently proofread by RNA cleavage. X-ray analysis reveals that a TU mismatch impairs RNA extension by forming a wobble base pair at the Pol II active center that dissociates the catalytic metal ion and misaligns the RNA 3' end. The mismatch can also stabilize a paused state of Pol II with a frayed RNA 3' nucleotide. The frayed nucleotide binds in the Pol II pore either parallel or perpendicular to the DNA-RNA hybrid axis (fraying sites I and II, respectively) and overlaps the nucleoside triphosphate (NTP) site, explaining how it halts transcription during proofreading, before backtracking and RNA cleavage.
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===Complete RNA polymerase II elongation complex III with a T-U mismatch and a frayed RNA 3'-uridine===
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Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.,Sydow JF, Brueckner F, Cheung AC, Damsma GE, Dengl S, Lehmann E, Vassylyev D, Cramer P Mol Cell. 2009 Jun 26;34(6):710-21. PMID:19560423<ref>PMID:19560423</ref>
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{{ABSTRACT_PUBMED_19560423}}
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==About this Structure==
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<div class="pdbe-citations 3how" style="background-color:#fffaf0;"></div>
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[[3how]] is a 15 chain structure of [[RNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HOW OCA].
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==See Also==
==See Also==
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*[[RNA polymerase|RNA polymerase]]
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:019560423</ref><references group="xtra"/>
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__TOC__
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[[Category: DNA-directed RNA polymerase]]
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Brueckner, F.]]
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[[Category: Brueckner F]]
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[[Category: Cheung, A C.M.]]
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[[Category: Cheung ACM]]
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[[Category: Cramer, P.]]
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[[Category: Cramer P]]
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[[Category: Damsma, G E.]]
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[[Category: Damsma GE]]
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[[Category: Dengl, S.]]
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[[Category: Dengl S]]
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[[Category: Lehmann, E.]]
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[[Category: Lehmann E]]
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[[Category: Sydow, J F.]]
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[[Category: Sydow JF]]
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[[Category: Vassylyev, D.]]
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[[Category: Vassylyev D]]
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[[Category: Dna damage]]
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[[Category: Dna repair]]
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[[Category: Dna-binding]]
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[[Category: Dna-directed rna polymerase]]
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[[Category: Dna-rna mismatch]]
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[[Category: Elongation complex]]
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[[Category: Isopeptide bond]]
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[[Category: Magnesium]]
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[[Category: Metal-binding]]
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[[Category: Mrna processing]]
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[[Category: Nucleotidyltransferase]]
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[[Category: Nucleus]]
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[[Category: Phosphoprotein]]
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[[Category: Rna fraying]]
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[[Category: Rna polymerase ii]]
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[[Category: Transcription]]
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[[Category: Transcription bubble]]
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[[Category: Transferase]]
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[[Category: Transferase-dna-rna hybrid complex]]
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[[Category: Zinc-finger]]
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Current revision

Complete RNA polymerase II elongation complex III with a T-U mismatch and a frayed RNA 3'-uridine

PDB ID 3how

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Proteopedia Page Contributors and Editors (what is this?)

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