3D structure of AraC (Escherichia coli)

The 292 residue AraC protein consists of two domains joined by a linker of at least five residues. The C-terminal domain of AraC is the DNA-binding domain.
The N-terminal domain of AraC binds arabinose and mediates dimerization.
AraC is a dimer in presence and in absence of arabinose. The binding of arabinose to AraC probably alters the conformation of the dimer impeding to contact distant DNA half-sites.

Only the N-terminal domain of AraC has been crystallized. There are two crystals for this domain:

1- Crystal of arabinose-binding and dimerization domain of the AraC protein with arabinose of Escherichia coli
    (PDB: 2ARC)

2- Crystal of arabinose-binding and dimerization domain of the AraC protein without arabinose of Escherichia coli
    (PDB: 2ARA)


1- Crystal of arabinose-binding and dimerization domain of the AraC protein with arabinose of Escherichia coli ( 2ARC )

Place the pointer in the figure over the part that you wish to identify.

The structure of this crystal at a resolution of 1'5 Amstrongs shows two monomers with 2 arabinose molecules.

Each monomer is made up of:
An N-terminal arm across the arabinose-binding pocket

A beta-barrel: composed by eight antiparallel beta-strands with jelly-roll topology.

A long linker: containing two 3(10) helix turns

The 9 beta strand: that also forms part of the beta-barrel

Alpha helix 1 and alpha-helix 2 (in red) packing against the outer surface of the beta-barrel

A pocket with alpha-L-arabinose (in yellow): The open end of the beta-barrel binds one molecule of arabinose in the full-chair conformation. Arabinose stacks the indole ring of Trp 95. Hydrogen bonds stabilize the binding of sugar. The N-terminal arm of AraC completes the binding site. It loops around to close off the end of the beta-barrel. Thus, arabinose is buried within AraC protein.


The AraC protein crystallized in presence of arabinose forms a dimer. The two monomers associate by an antiparallel coiled-coil between the two alpha-helices. A few adittional contacts exists between the 3(10) helices.

Each end of the coiled-coil is anchored by Leu-150 and Leu-151 with Leu-161 of the other monomer packing together in a knobs-into-holes manner.

The coiled-coil has a hydrophilic central core with polar side chains that establish hydrogen bonds between them and probably carry a water molecule buried at the helices interface.




2- Crystal of arabinose-binding and dimerization domain of AraC protein in absence of arabinose of Escherichia coli (2ARA)
In the absence of arabinose AraC crystallizes as a monomer in the crystallographic asymmetric unit.

The most noticeable difference between the structure of AraC with arabinose and unliganded AraC is the N-terminal arm. In absence of arabinose the N-terminal arm is disordered and it is not possible to determine it in the crystal.

When analyzing the crystal-packing two potential dimerization interfaces can be proposed. One is similar to the coiled-coil of the arabinose bound AraC , but with a distorsion in the top of the alpha-helix 2. The second dimer interface is formed by the beta-barrels of both AraC molecules. This dimer seems more plausible since it buries 75% more area than the other.
In this dimer Tyr-31 inserts its side chain in the sugar -binding site and packs against the indole ring of Trp-95.

At high concentrations of AraC protein without arabinose, both types of dimers should occur causing aggregation.

In the presence of arabinose, the NH2-terminal arms over the arabinose-binding pockets block the beta-barrel interaction.

The distance between the two COOH-terminuses is 60 Amstrongs in the beta-barrel dimer and 37 Amstrongs in the colied-coil dimer. This is in accordance with the fact that beta-barrel dimer binds two distant half-sites (O2 and I1) and coiled-coil dimer binds two close half-sites (I1 and I2). Probably in presence of arabinose the coiled-coil dimer is predominant and the beta-barrel dimer is plausible in absence of arabinose.


References:

Soisson SM, MacDougall-Shackleton B, Schleif R, Wolberger C.
Structural basis for ligand-regulated oligomerization of AraC.
Science. 1997 Apr 18;276(5311):421-5.
PMID: 9103202

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