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[[ | ==RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 5NT DNA-RNA HYBRID AND SOAKED WITH AMPCPP== | ||
<StructureSection load='4a3e' size='340' side='right' caption='[[4a3e]], [[Resolution|resolution]] 3.40Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4a3e]] 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=4A3E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4A3E FirstGlance]. <br> | |||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <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></td></tr> | |||
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1twc|1twc]], [[4a3k|4a3k]], [[1y77|1y77]], [[1r9s|1r9s]], [[1twg|1twg]], [[1sfo|1sfo]], [[4a3f|4a3f]], [[1i50|1i50]], [[4a3d|4a3d]], [[1r5u|1r5u]], [[1dzf|1dzf]], [[1y14|1y14]], [[1y1w|1y1w]], [[1nt9|1nt9]], [[1i3q|1i3q]], [[1pqv|1pqv]], [[1twf|1twf]], [[4a3g|4a3g]], [[4a3c|4a3c]], [[4a3i|4a3i]], [[4a3b|4a3b]], [[1i6h|1i6h]], [[1y1v|1y1v]], [[1y1y|1y1y]], [[1wcm|1wcm]], [[4a3m|4a3m]], [[1twa|1twa]], [[1nik|1nik]], [[2vum|2vum]], [[1twh|1twh]], [[1r9t|1r9t]], [[2ja7|2ja7]], [[2ja6|2ja6]], [[4a3l|4a3l]], [[1a1d|1a1d]], [[1k83|1k83]], [[2b63|2b63]], [[2b8k|2b8k]], [[2ja8|2ja8]], [[2ja5|2ja5]], [[4a3j|4a3j]]</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=4a3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4a3e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4a3e RCSB], [http://www.ebi.ac.uk/pdbsum/4a3e PDBsum]</span></td></tr> | |||
<table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
During transcription initiation by RNA polymerase (Pol) II, a transient open promoter complex (OC) is converted to an initially transcribing complex (ITC) containing short RNAs, and to a stable elongation complex (EC). We report structures of a Pol II-DNA complex mimicking part of the OC, and of complexes representing minimal ITCs with 2, 4, 5, 6, and 7 nucleotide (nt) RNAs, with and without a non-hydrolyzable nucleoside triphosphate (NTP) in the insertion site +1. The partial OC structure reveals that Pol II positions the melted template strand opposite the active site. The ITC-mimicking structures show that two invariant lysine residues anchor the 3'-proximal phosphate of short RNAs. Short DNA-RNA hybrids adopt a tilted conformation that excludes the +1 template nt from the active site. NTP binding induces complete DNA translocation and the standard hybrid conformation. Conserved NTP contacts indicate a universal mechanism of NTP selection. The essential residue Q1078 in the closed trigger loop binds the NTP 2'-OH group, explaining how the trigger loop couples catalysis to NTP selection, suppressing dNTP binding and DNA synthesis. | |||
Structural basis of initial RNA polymerase II transcription.,Cheung AC, Sainsbury S, Cramer P EMBO J. 2011 Nov 4. doi: 10.1038/emboj.2011.396. PMID:22056778<ref>PMID:22056778</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
==See Also== | |||
*[[RNA polymerase|RNA polymerase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
[[ | |||
== | |||
< | |||
[[Category: DNA-directed RNA polymerase]] | [[Category: DNA-directed RNA polymerase]] | ||
[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
Revision as of 11:35, 5 June 2014
RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 5NT DNA-RNA HYBRID AND SOAKED WITH AMPCPPRNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 5NT DNA-RNA HYBRID AND SOAKED WITH AMPCPP
Structural highlights
Publication Abstract from PubMedDuring transcription initiation by RNA polymerase (Pol) II, a transient open promoter complex (OC) is converted to an initially transcribing complex (ITC) containing short RNAs, and to a stable elongation complex (EC). We report structures of a Pol II-DNA complex mimicking part of the OC, and of complexes representing minimal ITCs with 2, 4, 5, 6, and 7 nucleotide (nt) RNAs, with and without a non-hydrolyzable nucleoside triphosphate (NTP) in the insertion site +1. The partial OC structure reveals that Pol II positions the melted template strand opposite the active site. The ITC-mimicking structures show that two invariant lysine residues anchor the 3'-proximal phosphate of short RNAs. Short DNA-RNA hybrids adopt a tilted conformation that excludes the +1 template nt from the active site. NTP binding induces complete DNA translocation and the standard hybrid conformation. Conserved NTP contacts indicate a universal mechanism of NTP selection. The essential residue Q1078 in the closed trigger loop binds the NTP 2'-OH group, explaining how the trigger loop couples catalysis to NTP selection, suppressing dNTP binding and DNA synthesis. Structural basis of initial RNA polymerase II transcription.,Cheung AC, Sainsbury S, Cramer P EMBO J. 2011 Nov 4. doi: 10.1038/emboj.2011.396. PMID:22056778[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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