Relaxed State

Diagram 3: relaxed state of DesT bound to DNA and UFA ligand.

DesT-oleoyl-CoA binds to a 30-base duplex DNA containing the 18-base pair pseudopalindromic desCB promoter sequence (AGTgAACgcttGTTgACT).

The N-terminal binding domain consists of a helix-turn-helix motif - α2-L2-L3-α3.

While α2 acts as a platform spanning the major groove of the DNA duplex, the α3 act as the 'recognition' helix penetrating this groove. α1 binds to the adjacent minor groove.  The N-terminus of α4 within the ligand-binding domain is 7Å away from the DNA, as seen in diagram 3.

Diagram 4: interactions between amino acid residues within DesT and DNA. [Diagram taken from here.]

The DesT-DNA interface involves the phospates of the DNA backbone and specific interactions with a pair of guanine bases within each half site - guanidinium groups of Arg36 and Arg51 with G+3 and G-8 respectively.

The DNA is bent by 3.3˚ towards the protein and the B-DNA helix is slightly deformed at the recognition site ; widening of the major groove from 11.7Å to 12.1-13.4Å and the helical repeat increases from 34Å to 36Å, slightly unwinding the DNA.

The L-shaped oleoyl chain of the ligand is buried within the hydrophobic core of DesT. The kink in the 18:1 chain at the cis-9 double bond directs the chain toward the periphery - the distal end projects between α4 and α7, and phenylalanines 71, 96, 107 and 166 along with Leu169 form a phenyalanine-rich cluster directly above the kink and below the α6.

The C termini of α6 and α6' loosely associate via stacking interactions between Arg122 and Arg122' and an edge-to-face interaction between Tyr115 and Pro170' at the C terminus of α8.

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