VRC01 gp120 complex

Structural Features

Similarities to CD4 in complex with gp120. ToxT belongs to a family of transcriptional regulators headed by and known as AraC.^[1] The AraC family is characterized by a 100 amino acid region of sequence similarity that forms a with two helix-turn-helix motifs (one on either side of the black linker). ^[2] This DNA binding domain is composed of seven alpha helices. HTH1 is composed of alpha helices five and six, while HTH2 is composed of alpha helices eight and nine. The two HTH regions are linked by the very polar alpha helix seven(shown in black). The overall domain is located at the C-terminus.^[1] Assuming ToxT is similar in mechanism to other AraC proteins, helix six from HTH1 and helix nine from HTH2 become aligned with the help of helix seven. Helix seven is positioned to attach to the N terminal binding pocket(the polar linking region) to allow binding to major consecutive grooves of target DNA (specific promoters for virulence genes).^[1][1]. The conformation of helix seven is dependent on the ligand bound.

Similarities to other antibodies in complex with gp120. or "jelly-roll" with three other alpha helices (overall making up the ) contain a . This is made from several residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). This pocket contains a sixteen-carbon fatty acid positioned in a conformation such that its negatively charged carboxylate group forms salt bridges between K31 of the N-terminal domain, and K230 from the C-terminal domain. The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.^[1] This pocket contains a ligand: ^[1] which appears to have a negative effect on virulence when present in vitro. The cis-palmitoleate forms with residues K31 and K230 (for detail, see Figure 1B of: [2]). This unsaturated fatty acid, like other UFAs,[3] tend to inhibit genes under the control of ToxT. Specifically, the cis-palmitoleate (PAM) appears to change ToxT's conformation, and thus lower its ability to bind DNA and form dimers.^[1] The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. PAM brings K31 and K230 together from either end of the protein, and essentially closes off ToxT. K230 is at the end of helix seven, and binding to K31 causes helix six to be pulled into an unfavorable conformation that deters DNA binding. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, PAM is in lower concentration. At this point, charge-charge repulsion between K31 and K230 leads to a destabilization of the closed conformation of ToxT. This repulsion prompts the opening of the N and C terminal domains. The freedom of helices six and seven to find a favorable configuration allows DNA binding to occur.^[1]

MSA 1xtc

Other features. Though the structure shown is a monomer with two overall domains (N-terminal and C-terminal), ToxT tends to form a dimer.^[3] The preferred state of ToxT varies between promoters, but binding to the ctx promoter to generate cholera toxin appears to be possible only in the dimer form.^[4]ToxT binds to thirteen base pair sequences (can be single, direct, or inverted repeats) called toxboxes in order to activate their respective promoters.[4]

bcode=3gbg&template=ligands.html&l=1.1] is shown, which can be bound in the beta sheet barrel (as discussed above). This unsaturated fatty acid reduces virulence expression in Vibrio cholerae.