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[[Image:2nvz.gif|left|200px]]
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{{STRUCTURE_2nvz|  PDB=2nvz  |  SCENE=  }}
'''RNA Polymerase II elongation complex with UTP, updated 11/2006'''


==RNA Polymerase II elongation complex with UTP, updated 11/2006==
<StructureSection load='2nvz' size='340' side='right'caption='[[2nvz]], [[Resolution|resolution]] 4.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2nvz]] 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=2NVZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NVZ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 4.3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=2nvz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nvz OCA], [https://pdbe.org/2nvz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nvz RCSB], [https://www.ebi.ac.uk/pdbsum/2nvz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nvz ProSAT]</span></td></tr>
</table>
== Function ==
[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.
== 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/nv/2nvz_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/main_output.php?pdb_ID=2nvz ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
New structures of RNA polymerase II (pol II) transcribing complexes reveal a likely key to transcription. The trigger loop swings beneath a correct nucleoside triphosphate (NTP) in the nucleotide addition site, closing off the active center and forming an extensive network of interactions with the NTP base, sugar, phosphates, and additional pol II residues. A histidine side chain in the trigger loop, precisely positioned by these interactions, may literally "trigger" phosphodiester bond formation. Recognition and catalysis are thus coupled, ensuring the fidelity of transcription.


==Overview==
Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis.,Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD Cell. 2006 Dec 1;127(5):941-54. PMID:17129781<ref>PMID:17129781</ref>
New structures of RNA polymerase II (pol II) transcribing complexes reveal a likely key to transcription. The trigger loop swings beneath a correct nucleoside triphosphate (NTP) in the nucleotide addition site, closing off the active center and forming an extensive network of interactions with the NTP base, sugar, phosphates, and additional pol II residues. A histidine side chain in the trigger loop, precisely positioned by these interactions, may literally "trigger" phosphodiester bond formation. Recognition and catalysis are thus coupled, ensuring the fidelity of transcription.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
2NVZ is a [[Protein complex]] structure of sequences 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=2NVZ OCA].
</div>
<div class="pdbe-citations 2nvz" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis., Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD, Cell. 2006 Dec 1;127(5):941-54. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17129781 17129781]
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
[[Category: DNA-directed RNA polymerase]]
== References ==
[[Category: Protein complex]]
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Bushnell, D A.]]
[[Category: Synthetic construct]]
[[Category: Kaplan, C D.]]
[[Category: Bushnell DA]]
[[Category: Kornberg, R D.]]
[[Category: Kaplan CD]]
[[Category: Wang, D.]]
[[Category: Kornberg RD]]
[[Category: Westover, K D.]]
[[Category: Wang D]]
[[Category: Dna]]
[[Category: Westover KD]]
[[Category: Molecular machine]]
[[Category: Mrna]]
[[Category: Multiprotein complex]]
[[Category: Transcription]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 09:58:30 2008''
Retrieved from "https://proteopedia.org/2nvz"