Beta-Prime Subunit of Bacterial RNA Polymerase: Difference between revisions

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Catherine L Dornfeld, Michal Harel, Mark Hoelzer, Jaime Prilusky, Angel Herraez

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 The <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_rudder_1/2'>rudder</scene> (coral) stabilizes the dwDNA and upstream RNA/DNA hybrid with numerous sidechain interactions. Two <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_rudderarg_1/1'>arginine sidechains</scene> are shown contacting the dwDNA and RNA/DNA hybrid<ref name='elongation' />. The rudder meets the <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_clamp_1/2'>clamp helices</scene> (dark grey) which interact with the σ subunit of RNAP.
-The upstream internal chamber can accommodate a 9-bp RNA/DNA hybrid<ref name='elongation' />. The RNA/DNA hybrid encounters the <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_lid_1/2'>lid</scene> (light green) that sterically blocks continued elongation<ref name='elongation' />. The lid facilitates <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_lidcleavage_1/1'>cleavage of the hydrogen bond</scene>, releasing the growing RNA transcript into the exit channel. As the bond is cleaved, the template strand moves one position upstream through the active site channel. This process is called translocation. This allows the lone <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_acceptor_1/2'>unpaired template nucleotide</scene> to move into the +1 site adjacent to the active site where nucleotide addition occurs<ref name='elongation' />.
+The upstream internal chamber can accommodate a 9-bp RNA/DNA hybrid<ref name='elongation' />. The RNA/DNA hybrid encounters the <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_lid_1/2'>lid</scene> (light green) that sterically blocks continued elongation<ref name='elongation' />. The lid facilitates <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_lidcleavage_1/1'>cleavage of the hydrogen bond</scene>, releasing the growing RNA transcript into the exit channel. As the bond is cleaved, the template strand moves one position upstream through the active site channel. This process is called translocation. This allows the lone <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_acceptor_1/4'>unpaired template nucleotide</scene> to move into the +1 site adjacent to the active site where nucleotide addition occurs<ref name='elongation' />.
 <font size='3'>'''Nucleotide Addition'''</font>
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 <font size='3'>'''Catalysis'''</font>
-The <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_activesite_1/3'>active site</scene> consists of three highly conserved aspartate sidechains (Asp739, Asp741, Asp743) chelated to a magnesium ion (MgI) required for catalysis<ref name='loading' />. <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_mgions_1/2'>MgI and MgII</scene> (lime green) chelated to the NTP coordinate positioning of the NTP for catalysis<ref name='lehninger'>Nelson, D. L. & Cox, M. M. (2008). Lehninger principles of biochemistry (5th ed.). New York: W. H. Freeman and Company.
+The <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_activesite_1/4'>active site</scene> consists of three highly conserved aspartate sidechains (Asp739, Asp741, Asp743) chelated to a magnesium ion (MgI) required for catalysis<ref name='loading' />. <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_mgions_1/2'>MgI and MgII</scene> (lime green) chelated to the NTP coordinate positioning of the NTP for catalysis<ref name='lehninger'>Nelson, D. L. & Cox, M. M. (2008). Lehninger principles of biochemistry (5th ed.). New York: W. H. Freeman and Company.
 </ref>. The <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_threeprime_1/2'>3' hydroxyl</scene> of the RNA transcript has nucleophilic activity and attacks the alpha-phosphate of the NTP<ref name='lehninger' />. A phosphodiester bond forms between the RNA transcript and the alpha-phosphate, and the beta- and gamma-phosphates leave as a pyrophosphate group<ref name='lehninger' />. After catalysis the RNA/DNA hybrid moves in the <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_minus1site_1/2'>-1 site</scene>, and the ribonucleotide in this bond provides the 3’ hydroxyl for the next incoming NTP<ref name='elongation' />.
 </StructureSection>