The DNA-binding domain of BenM reveals the structural basis for the recognition of a T-N₁₁-A sequence motif by LysR-type transcriptional regulators

Abstract

LysR-type transcriptional regulators (LTTRs) play critical roles in metabolism and constitute the largest family of bacterial regulators. To understand protein-DNA interactions, atomic structures of the DNA-binding domain and linker-helix regions of a prototypical LTTR, BenM, were determined by X-ray crystallography. BenM structures with and without bound DNA reveal a set of highly conserved amino acids that interact directly with DNA bases. At the N-terminal end of the recognition helix (α3) of a winged-helix-turn-helix DNA-binding motif, several residues create hydrophobic pockets (Pro30, Pro31 and Ser33). These pockets interact with the methyl groups of two thymines in the DNA-recognition motif and its complementary strand, T-N11-A. This motif usually includes some dyad symmetry, as exemplified by a sequence that binds two subunits of a BenM tetramer (ATAC-N7-GTAT). Gln29 forms hydrogen bonds to adenine in the first position of the recognition half-site (ATAC). Another hydrophobic pocket defined by Ala28, Pro30 and Pro31 interacts with the methyl group of thymine, complementary to the base at the third position of the half-site. Arg34 interacts with the complementary base of the 3' position. Arg53, in the wing, provides AT-tract recognition in the minor groove. For DNA recognition, LTTRs use highly conserved interactions between amino acids and nucleotide bases as well as numerous less-conserved secondary interactions.

Activation of leuO by LrhA in Escherichia coli

“…B). According to this structural model residue 12D of LrhA presumably corresponds to arginine 4 of BenM of A. baylyi which interacts with the DNA backbone (Alanazi et al ., ). Thus, one may speculate that mutation of LrhA at negatively charged glutamic acid residue 12 to the neutral and polar asparagine may enhance DNA binding.…”

Crystal structure of the ligand‐binding domain of a LysR‐type transcriptional regulator: transcriptional activation via a rotary switch

“…A. Model of the OccR DNA binding domain (DBD), linker domain and bound DNA, using the homologous regions of BenM as a template (Alanazi et al ., ). B and C. Models of full‐length apoprotein (B) and holoprotein (C).…”

DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression

“…LeuO belongs to this category of proteins. As a LysR-like transcription factor, LeuO typically binds to regulatory sequences located between divergently transcribed genes, where it seeks a match to a very loose consensus binding site sequence: T-N 11 -A (Alanazi et al 2013;Schell 1993;Sheehan and Dorman 1998) (Fig. 3).…”