Structural studies of the LysR-type transcriptional regulator BenM DNA binding domain with its DNA regulatory regions
Alanazi, Amer Mayouf
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The LysR-type transcriptional regulator (LTTR) BenM is involved in controlling benzoate degradation in the soil bacterium Acinetobacter baylyi strain ADP1. The 1.8 Å resolution crystal structure of the unbound BenM DNA binding domain (BenM DBD) confirmed that the BenM DBD forms a compact globular domain composed of three helices with helix-turn-helix motif (α2-α3), a wing, and a long linker-helix. BenM DBD was crystallized with short oligonucleotides from its cognate benA and catB DNA promoters in two different crystal-packing arrangements. In these nucleic acid complexes, BenM DBD dimers span a large region of bent DNA where the DNA recognition helices (α2) of one dimer bind into two consecutive DNA major grooves in a sequence-dependent manner. The specific DNA major groove interactions that define the LTTR conserved recognition motif (T-N11-A) include van der Waals interactions of two proline residues at the N-terminal end of the recognition helices with the methyl groups of thymine bases within the recognition motif. Also involved in sequence specific interactions are the side chain of Gln 29 with the imino and amino groups of an adenine base respectively (5'-ATAC-3') and the side chain of Arg 34 with the carbonyl oxygen of guanine (5`-GTAT-3`) in the complementary strand. A wing interacts mainly with the phosphate backbone of the DNA minor groove and assists in the proper positioning of the N-terminal end of the recognition helix. The BenM DBD/catB site 1 complex demonstrated very tight crystal packing with face to face contacts similar to the natural protein-protein interactions. The arrangement of the two DNA duplexes was unique. Chains E and F run as two columns parallel to the crystallographic c cell axis and contact one of the symmetry related protein subunits. Chains G and H create an end-to-end continuous helix with other symmetry-related mates and run perpendicular to the crystallographic c cell axis. The linker helices of BenM DBD chains A and C cross one-another, whereas linker helices of B and D run parallel to A and D respectively. These unique crystal packing arrangements might be generated and perhaps stabilized by the association of two malonate molecules at the N-terminal ends of two monomers each from dimer.