Rob. RIGHT ORIGIN BINDING PROTEIN (Escherichia coli)

(PDB: 1D5Y)

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This is the 2.7 Amstrong crystal structure of the Rob protein bound to the micF promoter. This is the representation of the A chain of Rob that interacts in a specific manner with the micF DNA sequence, contacting the major groove with a helix and the DNA backbone with another helix.

The complex reveals two Helix-Turn-Helix (HTH) subdomains within Rob's N-terminal domain. Rob's C-terminal domain is similar to the GalT enzyme. Its function is unknown but it probably functions as a enzyme.

N- Helix-Turn-Helix (HTH) DNA-binding subdomain:
Rob inserts its N-HTH-subdomain into a DNA major groove over the A box. This subdomain has 3 helices:
Helix A: the most N-terminal
Helix B: It is formed uniquely by four residues 25-D, 26-N, 27-V and 28-A.
Helix C: It is the DNA-recognition helix that interacts with the A box. At this binding site Rob makes Van der Waals and hydrogen bonds with the base pairs. In contrast with the MarA crystal the DNA is unbent.

C-Helix-Turn-Helix (HTH) DNA-binding subdomain: This subdomain is formed by the E, F and G helices . The C-terminal HTH lies on the surface of the DNA helix where it contacts the phosphodiester backbone. Unlike MarA, in this crystal the Rob C-HTH sudomain does not specifically interact with the major groove of the B-box. It is probably related with straight conformation of DNA. Arg 90 from helix F forms a hydrogen bond with the phosphate of Thy. This binding presumably compensates for the lack of major groove interactions.

References:

Kwon HJ, Bennik MH, Demple B, Ellenberger T.
Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA.
Nat Struct Biol. 2000 May;7(5):424-30.
PMID: 10802742; UI: 20264525

The figures were prepared with WebLab Viewer (Molecular Simulations Inc.)