Fig. 2: Interactions between the promoter DNA −35 element and SigI6 in the RPo-SigI6 structure.
From: Structure of the transcription open complex of distinct σI factors
A Comparison of the DNA-binding modes of the SigI6C domain (red) and the σ4 domain in σA from Bacillus subtilis (PDB 7CKQ, gray). The helices in the helix-turn-helix (HTH) motifs are shown as cylinders. The two panels on the right demonstrate that when the structures are superimposed by the HTH motif, the respective NT strands of the DNA run in opposite directions (indicated by 5’→3’); when the structures are superimposed by the promoter DNAs, the HTH motifs exhibit a ~ 180° rotation. B The detailed interactions in major and minor grooves of the −35 element DNA. Residues involved in the interactions are shown as sticks. SigI6C, red; NT-strand DNA, light blue; T-strand DNA, orange. C Comparison of the DNA-binding modes in the SigI6C-promoter (red) recognition and that of a transcription repressor Lmo0178-operator DNA complex (PDB 5F7Q, gray) from Listeria monocytogenes. Lmo0178 is a dimer in the structure and one Lmo0178 molecule (Lmo0178-1) is superimposed with SigI6C. Residues H171 in SigI6 and K9 in Lmo0178, which similarly penetrate the minor groove are shown as sticks with labels. Lmo0178 contains a wing loop, which additionally binds to the upstream minor groove. D Activities of SigI6 mutants measured by the Bacillus subtilis heterologous reporter system. E In vitro transcriptional activities of SigI6 mutants and promoter mutants. The bars are filled with the following colors: green, wild-type and C167S mutant; yellow and orange, mutants for residues potentially interacting with minor and major grooves of the −35 element, respectively; gray, mutants of the −10 element or residues potentially interacting with the −10 element. Data are presented as mean values ± SD, and n = 3 biological replicates in D and E. Source data of D and E are provided as a Source data file.
