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.Alanazi, A.M., Neidle, E.L., Momany, C.
(2013) Acta Crystallogr.,Sect.D 69: 1995-2007
- PubMed: 24100318
- DOI: 10.1107/S0907444913017320
- Primary Citation of Related Structures:  4IHS
- PubMed Abstract:
- Distinct effector-binding sites enable synergistic transcriptional activation by BenM, a LysR-type regulator
Ezezika, O.C.,Haddad, S.,Clark, T.J.,Neidle, E.L.,Momany, C.
(2007) J.Mol.Biol. 367(3): 616
- Inducer responses of BenM, a LysR-type transcriptional regulator from Acinetobacter baylyi ADP1.
Craven, S.H.,Ezezika, O.C.,Haddad, S.,Hall, R.A.,Momany, C.,Neidle, E.L.
(2009) MOL.MICROBIOL. 72(4): 881
- Oligomerization of BenM, a LysR-type transcriptional regulator: structural basis for the aggregation of proteins in this family.r
Ezezika, O.C.,Haddad, S.,Neidle, E.L.,Momany, C.
(2007) Acta Crystallogr.,Sect.F 63(Pt 5): 361
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 ...
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.
Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, USA.