3ZQ7

The Structure of DNA-binding domain of response regulator from Escherichia coli K-12

3ZQ7 の概要

• エントリーDOI: 10.2210/pdb3zq7/pdb
• 関連するPDBエントリー: 1ZH2 1ZH4
• 分子名称: KDP OPERON TRANSCRIPTIONAL REGULATORY PROTEIN KDPE (2 entities in total)
• 機能のキーワード: transcription, response regulator
• 由来する生物種: ESCHERICHIA COLI
• 細胞内の位置: Cytoplasm : P21866
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 11781.59

構造登録者

Patil, D.N.,Tomar, S.,Kumar, P. (登録日: 2011-06-08, 公開日: 2012-03-21, 最終更新日: 2023-12-20)

主引用文献

Narayanan, A.,Paul, L.N.,Tomar, S.,Patil, D.N.,Kumar, P.,Yernool, D.A.
Structure-Function Studies of DNA Binding Domain of Response Regulator Kdpe Reveals Equal Affinity Interactions at DNA Half-Sites.
Plos One, 7:102-, 2012

PubMed Abstract: Expression of KdpFABC, a K(+) pump that restores osmotic balance, is controlled by binding of the response regulator KdpE to a specific DNA sequence (kdpFABC(BS)) via the winged helix-turn-helix type DNA binding domain (KdpE(DBD)). Exploration of E. coli KdpE(DBD) and kdpFABC(BS) interaction resulted in the identification of two conserved, AT-rich 6 bp direct repeats that form half-sites. Despite binding to these half-sites, KdpE(DBD) was incapable of promoting gene expression in vivo. Structure-function studies guided by our 2.5 Å X-ray structure of KdpE(DBD) revealed the importance of residues R193 and R200 in the α-8 DNA recognition helix and T215 in the wing region for DNA binding. Mutation of these residues renders KdpE incapable of inducing expression of the kdpFABC operon. Detailed biophysical analysis of interactions using analytical ultracentrifugation revealed a 2∶1 stoichiometry of protein to DNA with dissociation constants of 200±100 and 350±100 nM at half-sites. Inactivation of one half-site does not influence binding at the other, indicating that KdpE(DBD) binds independently to the half-sites with approximately equal affinity and no discernable cooperativity. To our knowledge, these data are the first to describe in quantitative terms the binding at half-sites under equilibrium conditions for a member of the ubiquitous OmpR/PhoB family of proteins.

PubMed: 22291906
DOI: 10.1371/JOURNAL.PONE.0030102

実験手法

X-RAY DIFFRACTION (2.52 Å)