1y1w: Difference between revisions

Revision as of 17:01, 21 February 2008

Complete RNA Polymerase II elongation complex

OverviewOverview

The crystal structure of the complete 12 subunit RNA polymerase (pol) II bound to a transcription bubble and product RNA reveals incoming template and nontemplate DNA, a seven base pair DNA/RNA hybrid, and three nucleotides each of separating DNA and RNA. The complex adopts the posttranslocation state and accommodates a cocrystallized nucleoside triphosphate (NTP) substrate. The NTP binds in the active site pore at a position to interact with a DNA template base. Residues surrounding the NTP are conserved in all cellular RNA polymerases, suggesting a universal mechanism of NTP selection and incorporation. DNA-DNA and DNA-RNA strand separation may be explained by pol II-induced duplex distortions. Four protein loops partition the active center cleft, contribute to embedding the hybrid, prevent strand reassociation, and create an RNA exit tunnel. Binding of the elongation factor TFIIS realigns RNA in the active center, possibly converting the elongation complex to an alternative state less prone to stalling.

About this StructureAbout this Structure

1Y1W is a Protein complex structure of sequences from Saccharomyces cerevisiae with and as ligands. Active as DNA-directed RNA polymerase, with EC number 2.7.7.6 Full crystallographic information is available from OCA.

ReferenceReference

Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS., Kettenberger H, Armache KJ, Cramer P, Mol Cell. 2004 Dec 22;16(6):955-65. PMID:15610738

Page seeded by OCA on Thu Feb 21 16:01:02 2008

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OCA

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-[[Image:1y1w.gif|left|200px]]<br /><applet load="1y1w" size="450" color="white" frame="true" align="right" spinBox="true"
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 caption="1y1w, resolution 4.&Aring;" />
 '''Complete RNA Polymerase II elongation complex'''<br />
 ==Overview==
-The crystal structure of the complete 12 subunit RNA polymerase (pol) II, bound to a transcription bubble and product RNA reveals incoming template, and nontemplate DNA, a seven base pair DNA/RNA hybrid, and three, nucleotides each of separating DNA and RNA. The complex adopts the, posttranslocation state and accommodates a cocrystallized nucleoside, triphosphate (NTP) substrate. The NTP binds in the active site pore at a, position to interact with a DNA template base. Residues surrounding the, NTP are conserved in all cellular RNA polymerases, suggesting a universal, mechanism of NTP selection and incorporation. DNA-DNA and DNA-RNA strand, separation may be explained by pol II-induced duplex distortions. Four, protein loops partition the active center cleft, contribute to embedding, the hybrid, prevent strand reassociation, and create an RNA exit tunnel., Binding of the elongation factor TFIIS realigns RNA in the active center, possibly converting the elongation complex to an alternative state less, prone to stalling.
+The crystal structure of the complete 12 subunit RNA polymerase (pol) II bound to a transcription bubble and product RNA reveals incoming template and nontemplate DNA, a seven base pair DNA/RNA hybrid, and three nucleotides each of separating DNA and RNA. The complex adopts the posttranslocation state and accommodates a cocrystallized nucleoside triphosphate (NTP) substrate. The NTP binds in the active site pore at a position to interact with a DNA template base. Residues surrounding the NTP are conserved in all cellular RNA polymerases, suggesting a universal mechanism of NTP selection and incorporation. DNA-DNA and DNA-RNA strand separation may be explained by pol II-induced duplex distortions. Four protein loops partition the active center cleft, contribute to embedding the hybrid, prevent strand reassociation, and create an RNA exit tunnel. Binding of the elongation factor TFIIS realigns RNA in the active center, possibly converting the elongation complex to an alternative state less prone to stalling.
 ==About this Structure==
-Y1W 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 ZN and MG 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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1Y1W OCA].
+Y1W 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 <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=MG:'>MG</scene> 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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y1W OCA].
 ==Reference==
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 [[Category: Protein complex]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Armache, K.J.]]
+[[Category: Armache, K J.]]
 [[Category: Cramer, P.]]
 [[Category: Kettenberger, H.]]
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 [[Category: transcription bubble]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 06:30:16 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:01:02 2008''