Extended Data Fig. 6. Structural analysis of the interaction between UvrD-CTD and RNAP.

a, UvrD and RNAP β subunit domains observed in crystals structure were colored and labeled. b, The overall structure of the UvrD-CTD/RNAP-β2i4 (PDB 7EGS) binary complex. The major interface is highlighted by a rectangle. The ‘N’ and ‘C’ termini of UvrD-CTD are numbered. c, Detailed interactions between UvrD-CTD and RNAP-β2i4. Oxygen, nitrogen, and water atoms are colored in red, blue, and orange, respectively. Blue dash, H-bond. d, YTH results show that alanine substitution of interface residues on UvrD-CTD or βi4 impairs the interaction of UvrD and RNAP β pincer. The potential interactions were selected on SD (-HALW) plates, and the growth on SD (-LW) plates was used as input control, e, Strep-tag pull down results show that alanine substitution of interface residues of UvrD-CTD or βi4 impairs interaction between RNAP and UvrD. f, Sequence alignments of UvrD-CTD and RNAP-β2i4 from 316 non-redundant proteobacteria that contain βi4 insertion on RNAP. The key interface residues were labeled with blue asterisks and numbered as in E. coli. g, Cys pair cross-linking results demonstrate direct proximity of UvrD-CTD and RNAP-βi4. The wild-type or mutated UvrD-RNAP complexes were incubated in oxidative (CuCl₂) or reducing (DTT) condition and separated by SDS-PAGE. The asterisk marks two major impurity bands. The position of residues E690 of UvrD and N357 of RNAP β2 are labeled in (b).