Fig. 3: Ap4A bound in de novo transcription initiation complexes.
From: Molecular insight into 5′ RNA capping with NpnNs by bacterial RNA polymerase
a, AS structure of de novo transcription initiation, where Ap4A proximal adenine binds canonically in the i site. GMPcPP is bound in a preinsertion position in the i + 1 site. The DNA template strand is antiscrunched by one nucleotide relative to the AS and to the nontemplate strand. The aspartate triad of the AS coordinates MgA and β′/D739 coordinates MgB. Conserved residues β/K838 and K846 reach toward the Ap4A α phosphate and β/H999 and Q567 reach towards the Ap4A γ phosphate; β/Y998 points away from Ap4A. The distal adenine does not base pair with the −2G base of the template in the i − 1 site and flanks. Color coding as in Fig. 1. b, Cryo-EM density for Ap4A (gray) and template (blue). The proximal adenine base in the i site WC base pairs with template −1T. The distal adenine base flanks. c, AS structure of de novo transcription initiation, where Ap4A proximal adenine binds canonically in the i site and the distal adenine binds noncanonically in the i − 1 site. The depiction is analogous to a. Conserved residues β/K838 and K846 reach toward the Ap4A α phosphate, H999 reaches toward the Ap4A γ phosphate and β/Q567 reaches toward both γ and δ phosphates of the Ap4A; β/Y998 points away from Ap4A. d, Cryo-EM density for Ap4A (gray) and template (blue). The proximal adenine base in the i site WC base pairs with template +1T. The distal adenine base in the i − 1 site rWC base pairs with template −1T. e, Comparison of triphosphate and tetraphosphate linkers in TC-Ap3G (green) and aTT-Ap4A (gray) structures. Phosphorus atoms are highlighted as orange spheres. Nonbridging oxygen atoms of phosphates are omitted for clarity.
