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

<scene name='User:Catherine_L_Dornfeld/Sandbox_1/2o5j_dna_1/2'>DNA</scene> in the active site channel provides the genetic information for RNA transcription. The active site channel is 27 Å wide and accommodates both <scene name='User:Catherine_L_Dornfeld/Sandbox_1/2o5j_dwdna_1/2'>downstream DNA</scene> (dwDNA) and an <scene name='User:Catherine_L_Dornfeld/Sandbox_1/2o5j_hybrid_1/2'>RNA/DNA hybrid</scene><ref>PMID: 10499798</ref>. The <scene name='User:Catherine_L_Dornfeld/Sandbox_1/2o5j_template_1/1'>DNA template strand</scene> (blue) provides the complementary sequence for the RNA transcript and threads through the active site channel adjacent to the active site. The <scene name='User:Catherine_L_Dornfeld/Sandbox_1/2o5j_nontemplate_1/1'>non-template strand</scene> (dark blue), or coding strand, is held away from the active site by the clamp helices and rudder.  

The template strand is kinked at the junction between the dwDNA and RNA/DNA hybrid<ref name='elongation'>PMID: 17581590</ref>. The lone unpaired acceptor template base at the <scene name='User:Catherine_L_Dornfeld/Sandbox_1/2o5j_kink_1/1'>+1 site</scene> is located at the kink<ref name='elongation' />. The base pair at the <scene name='User:Catherine_L_Dornfeld/Sandbox_1/2o5j_plus2site_1/1'>+2 site</scene> is distorted<ref name='elongation' />. Upstream of the kink is the <scene name='User:Catherine_L_Dornfeld/Sandbox_1/2o5j_hybrid_1/2'>RNA/DNA hybrid</scene>. This hybrid structure is comprised of the template strand and the complementary RNA transcript connected by hydrogen bonds. The most recently formed hybrid bond is located at the <scene name='User:Catherine_L_Dornfeld/Sandbox_1/2o5j_minus1site_1/1'>-1 site</scene><ref name='elongation' />.   

The <scene name='User:Catherine_L_Dornfeld/Sandbox_1/2o5j_rudder_1/1'>rudder</scene> (coral) stabilizes the dwDNA and upstream RNA/DNA hybrid with numerous sidechain interactions. Two <scene name='User:Catherine_L_Dornfeld/Sandbox_1/2o5j_rudderarg_1/1'>arginine sidechains</scene> are shown contacting the dwDNA and RNA/DNA hybrid<ref name='elongation' />. The rudder meets the <scene name='User:Catherine_L_Dornfeld/Sandbox_1/2o5j_clamp_1/1'>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='User:Catherine_L_Dornfeld/Sandbox_1/2o5j_lid_1/1'>lid</scene> (light green) that sterically blocks continued elongation<ref name='elongation' />. The lid facilitates <scene name='User:Catherine_L_Dornfeld/Sandbox_1/2o5j_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='User:Catherine_L_Dornfeld/Sandbox_1/2o5j_acceptor_1/1'>unpaired template nucleotide</scene> to move into the +1 site adjacent to the active site where nucleotide addition occurs<ref name='elongation' />.