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Figure 2
Sequence specific binding of the 4 bp promoter consensus region within the non-template strand by the β-like subunit GP123. (A) Internal view of the non-template strand 5′-TATG-3′ consensus sequence running through the surface pocket within the β-like subunit GP123, between the β-lobe and well ordered polymerase core. Low-resolution continuations of the DNA chain are shown as dotted lines, while the modelled bases are labelled. (B) The structure of the binding pocket around the non-template strand. Key interacting side chains and stretches of backbone from GP123 are shown and numbered, while the consensus nucleotides are labelled. (C) The rotation of the β-lobe against the GP123 core in the ΦKZ nvRNAP promoter analogue and transcribing structures (in darker green), showing the 8° rotation opening the pocket for consensus DNA sequence binding. (D) The uracil-dependent binding mode of the AR9 nvRNAP to its own four-nucleotide consensus sequence (highlighted within a dotted red enclosure) is shown for comparison. This takes place principally in a pocket within the σ-factor-like subunit, rather than the β-like subunit, and towards the template strand, rather than the non-template strand, and is highly divergent from ΦKZ promoter consensus recognition. (E) Electrostatic isosurface of the GP123 pocket, showing the deep intrusion of the bases and charge complementation of the backbone phosphate residues and base functional groups. Protein and DNA are visualized according to the Fig. 1[link] colour scheme.

IUCrJ
Volume 13| Part 1| January 2026| Pages 31-43
ISSN: 2052-2525
https://doi.org/10.1107/S2052252525009273