Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution

Structure and function of the initially transcribing RNA polymerase II–TFIIB complex

“…The sigma factor is topologically related to TFIIB 1,2 and contains the loop region 3.2, which resembles the B-reader loop in location and negative charge [6][7][8] . Region 3.2 is required for formation of the first RNA phosphodiester bond, normal abortive transcription and sigma factor release [6][7][8] .…”

“…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 5 , and the bacterial initiation factor sigma has TFIIB-like topology 1,2 and contains the loop region 3.2 that resembles the B-reader loop in location, charge and function [6][7][8] . 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.…”

DNA Binding Specificity of Mu Transcription Factor C and Crystallization of C : DNA Complex

“…There are four flexible domains in σ 70 referred to as σ 1.1 , σ 2 , σ 3 and σ 4 (Helmann and Chamberlin, 1988) ( Figure 1-1). Each domain contains one or more highly conserved regions; 1.1 and 1.2, 2.1-2.4, 3.1-3.2 and 4.1-4.2 (Malhotra et al, 1996;Gross, 1998;Borukhov and Severinov, 2002;Campbell et al, 2002;Murakami et al, 2002;Vassylyev et al, 2002;Murakami and Darst, 2003). The σ 70 makes sequence-specific contacts within the -10 hexamer (consensus TATAAT) and -35 hexamer (consensus TTGACA) of the promoter using region 2.4 and region 4.2 only when σ 70 is bound to the core RNAP.…”

“…The bacterial RNAP holoenzyme structure has been solved from Thermus aquaticus and Thermus thermophilus (Murakami et al, 2002;Vassylyev et al, 2002).…”

“…The two sides of the claw are made up of β and β′, which also form the active site channel with a diameter of 27 Å. The entire length of the active-site channel is occupied by σ, and the negatively charged amino-acids of σ 1.1 and σ 3.2 occupy the upper and lower portions of the active-site channel, respectively (Mekler et al, 2002;Murakami et al, 2002;Vassylyev et al, 2002). These charged amino-acids mask the positively-charged portion of the channel, thus narrowing the channel and preventing nonspecific binding of RNAP to DNA.…”