Place the pointer on the figure over the part that you wish to identify.
MarA is composed of seven alpha helices and folds into two structurally similar subdomains with a long C-terminal loop.
N-Helix-Turn-Helix (HTH) DNA-binding subdomain:
This subdomain is formed by helix1, helix 2 and helix 3. Helices 1 and 2 are antiparallel and almost perpendicular to helix 3.
C- Helix-Turn-Helix (HTH) DNA-binding subdomain:
This subdomain is composed by helix 4, helix 5 and helix 6. Helices 4 and 5 are antiparallel and almost perpendicular to helix 6.
Helix 3: is one of the DNA recognition helices. It inserts into a DNA major groove with the axis of the alpha helix almost parallel to the DNA base pairs.
Helix 6: is the other DNA recognition helix. It inserts into an adjacent DNA major groove in a similar disposition to helix 3.
Helix 4: connects the two HTH subdomains imposing the orienation and distance restraints on the two DNA-binding subdomains.Helix 4 establishes a separation of 27 Amstrongs between the DNA recognition helix 3 and helix 6. Since the pitch of B-form of the DNA is 34 Amstrongs, the binding to MarA distorts the DNA structure.
Two DNA kinks are observed near G-10 and G-20 resulting in an overall bend of 35º in the DNA toward MarA.
References:
Rhee S, Martin RG, Rosner JL, Davies DR.
A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator.
Proc Natl Acad Sci U S A. 1998 Sep 1;95(18):10413-8.
PMID: 9724717; UI: 98393658
The figures were prepared with WebLab Viewer (Molecular Simulations Inc.)