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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 '''[[RNA polymerase]]''' (RNAP) is a molecular machine that copies DNA into RNA comprised and is found in every living organism. The bacterial RNAP complex consists of six subunits (ββ’α2ωσ) and three channels. RNAP initially binds to DNA at the promoter, forming the closed complex<ref name='genetics'>Snyder, L. & Champness, W. (2007). Molecular genetics of bacteria (3rd ed.). Washington, D.C.: ASM Press.</ref>. The DNA surrounding the promoter sequence unwinds and forms the open complex (http://www.pingrysmartteam.com/RPo/RPo.htm - please note that different nomenclature is used)<ref>2006 Pingry SMART Team: RNA Polymerase Holoenzyme Open Promoter Complex (Rpo) Jmol Tutorial</ref>. RNAP releases from the promoter and transitions into the elongation complex (EC). The EC moves along the template strand, adding ribonucleotides to the 3’ hydroxyl of the RNA transcript.
-This tutorial uses the β’ subunit of the RNAP elongation complex of ''Thermus thermophilus''. The β’ subunit contains structures crucial to transcription, including the sites for ribonucleotide addition and catalysis. Double-stranded DNA (dwDNA) enters RNAP through the active site channel, while ribonucleotides (NTPs) enter through the secondary channel. As the dwDNA enters, it separates into the template and non-template strands. The template strand forms an approximately 90 degree kink in the active site channel. At the kink, one DNA base pair becomes available for NTP pairing and translocates to the +1 site. An NTP enters the active site and induces conformational change of the trigger loop into the trigger helix. The trigger helix forms a three-helical bundle with the bridge helix. This bundle changes dimensions of the active site and facilitates positioning of the NTP for addition to the growing RNA strand. Upon addition of the nucleotide, the dwDNA and RNA/DNA hybrid translocate through RNAP with stabilization from the rudder. The growing RNA strand is separated by the lid and exits RNAP through the exit channel. The DNA template strand rejoins the non-template strand as it exits the active site channel.
+This tutorial uses the β’ subunit of the RNAP elongation complex of ''Thermus thermophilus''. The β’ subunit contains structures crucial for transcription, including the sites for ribonucleotide addition and catalysis. Double-stranded DNA (dwDNA) enters RNAP through the active site channel, while ribonucleotides (NTPs) enter through the secondary channel. As the dwDNA enters, it separates into the template and non-template strands. The template strand forms an approximately 90 degree kink in the active site channel. At the kink, one DNA base pair becomes available for NTP pairing and translocates to the +1 site. An NTP enters the active site and induces conformational change of the trigger loop into the trigger helix. The trigger helix forms a three-helical bundle with the bridge helix. This bundle changes dimensions of the active site and facilitates positioning of the NTP for addition to the growing RNA strand. Upon addition of the nucleotide, the dwDNA and RNA/DNA hybrid translocate through RNAP with stabilization from the rudder. The growing RNA strand is separated by the lid and exits RNAP through the exit channel. The DNA template strand rejoins the non-template strand as it exits the active site channel.
 '''Video 1: RNA Polymerase Elongation Complex'''