Figure 2.

Conformations of the bridge helix (BH) observed in crystal structures of multisubunit RNAPs. (a) Kinked orientation of the BH in some Tth RNAP crystal structures. BH from Tth RNAP holoenzyme without nucleic acids [PDB:1iw7] (cyan) [8]. BH from Tth holoenzyme without nucleic acids [PDB:2cw0] (slate blue) [9]. BH from Tth holoenzyme without nucleic acids in the presence of streptolydigin [PDB:1zyr] (yellow) [9]. (b) Straight orientation of the BH in Tth elongation complex structures with or without nucleoside triphosphate (NTP) substrate. BH from the Tth transcribing complex without NTP substrate (the trigger loop (TL) in this structure is in the 'out' position away from the substrate-addition site) [PDB:2o5i] (orange) [10]. BH from Tth elongation complex with NTP substrate (the TL is folded 'in' and contacting the NTP substrate in this structure) [PDB:ID 2o5j] (lime green) [2]. (c) Mild perturbation of the Pol II BH in elongation complex with matched NTP substrate in position for addition. BH from S. cerevisiae (Sce) Pol II elongation complex without substrate, PDB 1i6h (magenta) [11]. BH from the Sce Pol II elongation complex with mismatched substrate (the TL is in the 'out' position away from substrate-addition site in this structure) [PDB:1r9t] (teal) [5]. BH from the Sce Pol II elongation complex with matched substrate (the TL is folded 'in' and contacting the NTP substrate in this structure) [PDB:2e2h] (blue) [3]. This figure was created with PyMOL.

Kaplan and Kornberg Journal of Biology 2008 7:39   doi:10.1186/jbiol99
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