4IHS

Crystal Structure of BenM_DBD/catB site 1 DNA Complex

Summary for 4IHS

• Entry DOI: 10.2210/pdb4ihs/pdb
• Related: 3M1E 4IHT
• Descriptor: HTH-type transcriptional regulator BenM, catB site 1 DNA, catB site 1 DNA - complement, ... (6 entities in total)
• Functional Keywords: whth, hth, transcriptional regulator, catb promoter, transcription-dna complex, transcription/dna
• Biological source: Acinetobacter sp.; More
• Total number of polymer chains: 8
• Total formula weight: 74677.35

Authors

Alanazi, A.,Momany, C.,Neidle, E.L. (deposition date: 2012-12-19, release date: 2013-07-10, Last modification date: 2023-09-20)

Primary citation

Alanazi, A.M.,Neidle, E.L.,Momany, C.
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.
Acta Crystallogr.,Sect.D, 69:1995-2007, 2013

PubMed 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.

PubMed: 24100318
DOI: 10.1107/S0907444913017320

Experimental method

X-RAY DIFFRACTION (3.1 Å)