2ja6

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[[Image:2ja6.gif|left|200px]]<br />
 
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<applet load="2ja6" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2ja6, resolution 4.0&Aring;" />
 
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'''CPD LESION CONTAINING RNA POLYMERASE II ELONGATION COMPLEX B'''<br />
 
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==Overview==
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==CPD lesion containing RNA Polymerase II elongation complex B==
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Cells use transcription-coupled repair (TCR) to efficiently eliminate DNA, lesions such as ultraviolet light-induced cyclobutane pyrimidine dimers, (CPDs). Here we present the structure-based mechanism for the first step, in eukaryotic TCR, CPD-induced stalling of RNA polymerase (Pol) II. A CPD, in the transcribed strand slowly passes a translocation barrier and enters, the polymerase active site. The CPD 5'-thymine then directs uridine, misincorporation into messenger RNA, which blocks translocation., Artificial replacement of the uridine by adenosine enables CPD bypass;, thus, Pol II stalling requires CPD-directed misincorporation. In the, stalled complex, the lesion is inaccessible, and the polymerase, conformation is unchanged. This is consistent with nonallosteric, recruitment of repair factors and excision of a lesion-containing DNA, fragment in the presence of Pol II.
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<StructureSection load='2ja6' size='340' side='right'caption='[[2ja6]], [[Resolution|resolution]] 4.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2ja6]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JA6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JA6 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]] 4&#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=TT:[(1R,3R,4S,9R,10S,12R,15aS,15bR,18bR,18cS)-10-hydroxy-15a,15b-dimethyl-13,15,16,18-tetraoxohexadecahydro-8H-9,12-epoxy-1,4-methano-2,5,7-trioxa-12a,14,17,18a-tetraazacyclohexadeca[1,2,3,4-def]biphenylen-3-yl]methyl+dihydrogen+phosphate'>TT</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=2ja6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ja6 OCA], [https://pdbe.org/2ja6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ja6 RCSB], [https://www.ebi.ac.uk/pdbsum/2ja6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ja6 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RPB3_YEAST RPB3_YEAST] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft. Seems to be involved in transcription termination.
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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/ja/2ja6_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=2ja6 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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Cells use transcription-coupled repair (TCR) to efficiently eliminate DNA lesions such as ultraviolet light-induced cyclobutane pyrimidine dimers (CPDs). Here we present the structure-based mechanism for the first step in eukaryotic TCR, CPD-induced stalling of RNA polymerase (Pol) II. A CPD in the transcribed strand slowly passes a translocation barrier and enters the polymerase active site. The CPD 5'-thymine then directs uridine misincorporation into messenger RNA, which blocks translocation. Artificial replacement of the uridine by adenosine enables CPD bypass; thus, Pol II stalling requires CPD-directed misincorporation. In the stalled complex, the lesion is inaccessible, and the polymerase conformation is unchanged. This is consistent with nonallosteric recruitment of repair factors and excision of a lesion-containing DNA fragment in the presence of Pol II.
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==About this Structure==
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CPD damage recognition by transcribing RNA polymerase II.,Brueckner F, Hennecke U, Carell T, Cramer P Science. 2007 Feb 9;315(5813):859-62. PMID:17290000<ref>PMID:17290000</ref>
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2JA6 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with MG and ZN as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Structure known Active Site: AC1. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2JA6 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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CPD damage recognition by transcribing RNA polymerase II., Brueckner F, Hennecke U, Carell T, Cramer P, Science. 2007 Feb 9;315(5813):859-62. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17290000 17290000]
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</div>
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[[Category: DNA-directed RNA polymerase]]
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<div class="pdbe-citations 2ja6" style="background-color:#fffaf0;"></div>
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[[Category: Protein complex]]
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[[Category: Saccharomyces cerevisiae]]
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[[Category: Brueckner, F.]]
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[[Category: Carell, T.]]
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[[Category: Cramer, P.]]
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[[Category: Hennecke, U.]]
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[[Category: MG]]
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[[Category: ZN]]
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[[Category: arrest]]
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[[Category: cpd]]
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[[Category: cyclobutane pyrimidine dimer]]
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[[Category: damage recognition]]
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[[Category: dna damage]]
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[[Category: dna lesion]]
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[[Category: dna-binding]]
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[[Category: dna-directed rna polymerase]]
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[[Category: elongation complex]]
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[[Category: lesion recognition]]
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[[Category: metal-binding]]
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[[Category: misincorporation]]
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[[Category: nuclear protein]]
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[[Category: nucleotidyltransferase]]
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[[Category: phosphorylation]]
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[[Category: photolesion]]
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[[Category: rna polymerase ii]]
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[[Category: stalling]]
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[[Category: tcr]]
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[[Category: thymine dimer]]
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[[Category: transcription]]
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[[Category: transcription bubble]]
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[[Category: transcription- coupled repair]]
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[[Category: transferase]]
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[[Category: transferase/dna/rna]]
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[[Category: zinc]]
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[[Category: zinc-finger]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 12:29:47 2007''
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==See Also==
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Saccharomyces cerevisiae]]
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[[Category: Synthetic construct]]
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[[Category: Brueckner F]]
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[[Category: Carell T]]
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[[Category: Cramer P]]
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[[Category: Hennecke U]]

Current revision

CPD lesion containing RNA Polymerase II elongation complex B

PDB ID 2ja6

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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