4bbr: Difference between revisions
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[[ | ==Structure of RNA polymerase II-TFIIB complex== | ||
<StructureSection load='4bbr' size='340' side='right' caption='[[4bbr]], [[Resolution|resolution]] 3.40Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4bbr]] is a 13 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=4BBR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BBR FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1a1d|1a1d]], [[1dzf|1dzf]], [[1i3q|1i3q]], [[1i50|1i50]], [[1i6h|1i6h]], [[1k83|1k83]], [[1nik|1nik]], [[1nt9|1nt9]], [[1pqv|1pqv]], [[1r5u|1r5u]], [[1r9s|1r9s]], [[1r9t|1r9t]], [[1sfo|1sfo]], [[1twa|1twa]], [[1twc|1twc]], [[1twf|1twf]], [[1twg|1twg]], [[1twh|1twh]], [[1wcm|1wcm]], [[1y14|1y14]], [[1y1v|1y1v]], [[1y1w|1y1w]], [[1y1y|1y1y]], [[1y77|1y77]], [[2b63|2b63]], [[2b8k|2b8k]], [[2ja5|2ja5]], [[2ja6|2ja6]], [[2ja7|2ja7]], [[2ja8|2ja8]], [[2vum|2vum]], [[4a3b|4a3b]], [[4a3c|4a3c]], [[4a3d|4a3d]], [[4a3e|4a3e]], [[4a3f|4a3f]], [[4a3g|4a3g]], [[4a3i|4a3i]], [[4a3j|4a3j]], [[4a3k|4a3k]], [[4a3l|4a3l]], [[4a3m|4a3m]], [[4a93|4a93]], [[4bbs|4bbs]]</td></tr> | |||
<tr id='activity'><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 id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4bbr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bbr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4bbr RCSB], [http://www.ebi.ac.uk/pdbsum/4bbr PDBsum]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The general transcription factor (TF) IIB is required for RNA polymerase (Pol) II initiation and extends with its B-reader element into the Pol II active centre cleft. Low-resolution structures of the Pol II-TFIIB complex indicated how TFIIB functions in DNA recruitment, but they lacked nucleic acids and half of the B-reader, leaving other TFIIB functions enigmatic. Here we report crystal structures of the Pol II-TFIIB complex from the yeast Saccharomyces cerevisiae at 3.4 A resolution and of an initially transcribing complex that additionally contains the DNA template and a 6-nucleotide RNA product. The structures reveal the entire B-reader and protein-nucleic acid interactions, and together with functional data lead to a more complete understanding of transcription initiation. TFIIB partially closes the polymerase cleft to position DNA and assist in its opening. The B-reader does not reach the active site but binds the DNA template strand upstream to assist in the recognition of the initiator sequence and in positioning the transcription start site. TFIIB rearranges active-site residues, induces binding of the catalytic metal ion B, and stimulates initial RNA synthesis allosterically. TFIIB then prevents the emerging DNA-RNA hybrid duplex from tilting, which would impair RNA synthesis. When the RNA grows beyond 6 nucleotides, it is separated from DNA and is directed to its exit tunnel by the B-reader loop. Once the RNA grows to 12-13 nucleotides, it clashes with TFIIB, triggering TFIIB displacement and elongation complex formation. Similar mechanisms may underlie all cellular transcription because all eukaryotic and archaeal RNA polymerases use TFIIB-like factors, and the bacterial initiation factor sigma has TFIIB-like topology and contains the loop region 3.2 that resembles the B-reader loop in location, charge and function. TFIIB and its counterparts may thus account for the two fundamental properties that distinguish RNA from DNA polymerases: primer-independent chain initiation and product separation from the template. | |||
Structure and function of the initially transcribing RNA polymerase II-TFIIB complex.,Sainsbury S, Niesser J, Cramer P Nature. 2012 Nov 14. doi: 10.1038/nature11715. PMID:23151482<ref>PMID:23151482</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
==See Also== | |||
*[[RNA polymerase|RNA polymerase]] | |||
== | *[[Transcription initiation factor|Transcription initiation factor]] | ||
[[ | == References == | ||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: DNA-directed RNA polymerase]] | [[Category: DNA-directed RNA polymerase]] | ||
[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Cramer, P | [[Category: Cramer, P]] | ||
[[Category: Niesser, J | [[Category: Niesser, J]] | ||
[[Category: Sainsbury, S | [[Category: Sainsbury, S]] | ||
[[Category: Rna polymerase]] | [[Category: Rna polymerase]] | ||
[[Category: Tfiib]] | [[Category: Tfiib]] | ||
[[Category: Transcription]] | [[Category: Transcription]] | ||
Revision as of 17:47, 9 December 2014
Structure of RNA polymerase II-TFIIB complexStructure of RNA polymerase II-TFIIB complex
Structural highlights
Publication Abstract from PubMedThe general transcription factor (TF) IIB is required for RNA polymerase (Pol) II initiation and extends with its B-reader element into the Pol II active centre cleft. Low-resolution structures of the Pol II-TFIIB complex indicated how TFIIB functions in DNA recruitment, but they lacked nucleic acids and half of the B-reader, leaving other TFIIB functions enigmatic. Here we report crystal structures of the Pol II-TFIIB complex from the yeast Saccharomyces cerevisiae at 3.4 A resolution and of an initially transcribing complex that additionally contains the DNA template and a 6-nucleotide RNA product. The structures reveal the entire B-reader and protein-nucleic acid interactions, and together with functional data lead to a more complete understanding of transcription initiation. TFIIB partially closes the polymerase cleft to position DNA and assist in its opening. The B-reader does not reach the active site but binds the DNA template strand upstream to assist in the recognition of the initiator sequence and in positioning the transcription start site. TFIIB rearranges active-site residues, induces binding of the catalytic metal ion B, and stimulates initial RNA synthesis allosterically. TFIIB then prevents the emerging DNA-RNA hybrid duplex from tilting, which would impair RNA synthesis. When the RNA grows beyond 6 nucleotides, it is separated from DNA and is directed to its exit tunnel by the B-reader loop. Once the RNA grows to 12-13 nucleotides, it clashes with TFIIB, triggering TFIIB displacement and elongation complex formation. Similar mechanisms may underlie all cellular transcription because all eukaryotic and archaeal RNA polymerases use TFIIB-like factors, and the bacterial initiation factor sigma has TFIIB-like topology and contains the loop region 3.2 that resembles the B-reader loop in location, charge and function. TFIIB and its counterparts may thus account for the two fundamental properties that distinguish RNA from DNA polymerases: primer-independent chain initiation and product separation from the template. Structure and function of the initially transcribing RNA polymerase II-TFIIB complex.,Sainsbury S, Niesser J, Cramer P Nature. 2012 Nov 14. doi: 10.1038/nature11715. PMID:23151482[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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