Figure 6
From: The mechanism of a formaldehyde-sensing transcriptional regulator
Modeling the Pfrm–EcFrmR complex.
(a) The DNA sequence of the frmRAB promoter region (Pfrm) contains tandem EcFrmR binding sites consisting of ATAC/GTAT inverted repeats (bold) separated by G/C-rich tracts (italic) that form a larger inverted repeat (convergent red arrows). The size of EcFrmR (subunits colored in shades of green and orange as in Fig. 5b) suggests that two tetramers could bind to the frmRAB promoter region. One EcFrmR tetramer (side view) is shown on the top face of the DNA sequence and the other (top view) behind the DNA sequence, offset by approximately a quarter turn relative to the first tetramer. (b) Models of binary complexes formed from EcFrmR and A- or B-form DNA. One of the tandem EcFrmR binding sites of Pfrm (dark gray) is modeled as A- (left) and B-form (right) DNA. EcFrmR is shown as surface representation with subunits colored in shades of green (uncross-linked A/B face) and orange (cross-linked A′/B′ face), with the amino acid side-chains on the A/B face that are implicated in DNA-binding highlighted in blue.
