Electrostatic activation of Escherichia coli methionine repressor Kathryn Phillips, Simon EV Phillips  Structure  Volume 2, Issue 4, Pages 309-316 (April 1994) DOI: 10.1016/S0969-2126(00)00032-0

Figure 1 Overall fold of the holorepressor backbone, with the molecular dyad vertical. One subunit is shown in red with regions of secondary structure labelled, and the other in pink. The SAM molecules are shown as ball-and-stick models (green) with the sulphur atoms yellow, and bind to two symmetry- related sites at the bottom. Drawn with program MOLSCRIPT [16]. Structure 1994 2, 309-316DOI: (10.1016/S0969-2126(00)00032-0)

Figure 2 Sequence and numbering scheme for the operator oligonucleotide in the crystal structure of the complex. The two strands are related by a central crystallographic two-fold axis. The boxed regions correspond to consensus met boxes. Structure 1994 2, 309-316DOI: (10.1016/S0969-2126(00)00032-0)

Figure 3 Stereo view of repressor–operator complex. Two repressors (in red) are bound to the DNA at upper left and lower right respectively, and related by a crystallographic two-fold axis passing through the centre of the complex perpendicular to the plane of the paper. The SAM molecules (green) lie on the outer surface of the complex, distant from the DNA. The DNA is shown in a surface representation, coloured such that all atoms lying within the +1kT e −1 potential contour due to SAM partial charges are blue, while all atoms with a potential < +1kT e −1 are white. Structure 1994 2, 309-316DOI: (10.1016/S0969-2126(00)00032-0)

Figure 4 Chemical structures of S-adenosylmethionine (SAM), adenosylornithine (AO) and S-adenosylhomocysteine (SAH). The partial charges used in the calculation of the corepressor and corepressor analogue interactions with the operator DNA are shown in full for SAM. For AO and SAH, atom names are shown only where they differ from SAM. The charge sets were derived from the AMBER charges for methionine and adenosine. Structure 1994 2, 309-316DOI: (10.1016/S0969-2126(00)00032-0)

Figure 5 Contours of electrostatic potential of the holorepressor displayed as a slice through the molecule in the same orientation as Figure 1. The +1kT e−1 contour is blue, and the −1kT e−1 contour red. The repressor is green. A region of positive potential extends into the solvent from the β -ribbon DNA-binding face at the top of the molecule. The potential map for aporepressor (not shown) is superficially very similar. Structure 1994 2, 309-316DOI: (10.1016/S0969-2126(00)00032-0)

Figure 6 Map of the potential generated by SAM molecules when buried in the low dielectric cavity of the repressor–operator complex found in the crystal structure in the same orientation as Figure 3. The +1kT e−1 (blue) potential crosses the interface between the two repressor dimers, and extends through the complex to lie over an extended region of the phosphate backbone. The −1kT e−1 contour is shown in red, DNA in white. Structure 1994 2, 309-316DOI: (10.1016/S0969-2126(00)00032-0)

Figure 7 Comparison of the +1kT e−1 potential contours due to SAM (pink), SAH (blue) and AO (red) at phosphate P10 (3′ to A9) of the operator (white). The SAM contour extends furthest over the operator backbone, resulting in the most favourable interaction. Structure 1994 2, 309-316DOI: (10.1016/S0969-2126(00)00032-0)