Extended Data Fig. 9: The interactions of NtcB to promoter DNA and RNAP in NtcA-NtcB-TAC.
From: DNA looping mediates cooperative transcription activation
a, Superposition of NtcB-DBD/DNA in NtcA-NtcB-TAC and the crystal structure of BenM-DBD/DNA complex (PDB:4IHS). The residues of NtcB (blue, yellow) and BenM (black) responsible for DNA motif recognition are labeled. NT, nontemplate. b, Alanine mutation of the DNA motif-recognition residues (R34A/H53A; NtcBM) of NtcB abolished the binding ability of NtcB to a DNA fragment containing NtcB boxes. The EMSA results are representatives of > 3 independent experiments that showed similar results. Source data are provided in the Source Data file. c, Mutations of the DNA motif-recognition or RNAP-contact residues of NtcB impairs the transcription activation activity of NtcB. Data are presented as mean ± S.E.M., n = 3 biologically independent experiments. Two-tailed unpaired t-tests. No p value adjustments for multiple comparisons. The lower panel shows the representative gel image. **P < 0.05 indicates significant difference compared to lane 3. RNA transcripts, 102 nt. 2-OG, 2-oxoglutarate. △151–160, deletion of the contact patch (residues Leu151-Gly160) of NtcB. d, Cryo-EM map showing the interface between RNAP and NtcB-αNTD.
