4IHT

Crystal Structure of BenM_DBD/benA site 1 DNA Complex

4IHT の概要

• エントリーDOI: 10.2210/pdb4iht/pdb
• 関連するPDBエントリー: 3M1E 4IHS
• 分子名称: HTH-type transcriptional regulator BenM, benA site 1 DNA, benA site 1 DNA - complement, ... (4 entities in total)
• 機能のキーワード: whth, hth, transcriptional regulator, bena promoter site 1, transcription-dna complex, transcription/dna
• 由来する生物種: Acinetobacter sp.; 詳細
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 74450.27

構造登録者

Alanazi, A.,Momany, C.,Neidle, E.L. (登録日: 2012-12-19, 公開日: 2013-07-10, 最終更新日: 2023-09-20)

主引用文献

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

実験手法

X-RAY DIFFRACTION (3 Å)