3how

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[[Image:3how.png|left|200px]]
 
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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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The line below this paragraph, containing "STRUCTURE_3how", creates the "Structure Box" on the page.
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<StructureSection load='3how' size='340' side='right'caption='[[3how]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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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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or leave the SCENE parameter empty for the default display.
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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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{{STRUCTURE_3how| PDB=3how | SCENE= }}
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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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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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<div class="pdbe-citations 3how" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19560423}}, adds the Publication Abstract to the page
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19560423 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19560423}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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[[3how]] is a 15 chain structure 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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==Reference==
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<ref group="xtra">PMID:019560423</ref><references group="xtra"/>
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[[Category: DNA-directed RNA polymerase]]
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[[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: Cytoplasm]]
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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: Polymorphism]]
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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: Ubl conjugation]]
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[[Category: Zinc]]
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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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