7BBQ

Crystal structure of the HTH DNA binding protein ArdK from R388 plasmid. Apo form.

7BBQ の概要

• エントリーDOI: 10.2210/pdb7bbq/pdb
• 分子名称: KORA domain-containing protein (1 entity in total)
• 機能のキーワード: dna binding protein, helix turn helix, direct repeat, plasmid conjugation
• 由来する生物種: Escherichia coli K-12
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 12658.80

構造登録者

Fernandez-Lopez, R.,Boer, D.R.,Moncalian, G. (登録日: 2020-12-18, 公開日: 2022-07-13, 最終更新日: 2024-10-23)

主引用文献

Fernandez-Lopez, R.,Ruiz, R.,Del Campo, I.,Gonzalez-Montes, L.,Boer, D.R.,de la Cruz, F.,Moncalian, G.
Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors.
Nucleic Acids Res., 50:11938-11947, 2022

PubMed Abstract: Some transcription factors bind DNA motifs containing direct or inverted sequence repeats. Preference for each of these DNA topologies is dictated by structural constraints. Most prokaryotic regulators form symmetric oligomers, which require operators with a dyad structure. Binding to direct repeats requires breaking the internal symmetry, a property restricted to a few regulators, most of them from the AraC family. The KorA family of transcriptional repressors, involved in plasmid propagation and stability, includes members that form symmetric dimers and recognize inverted repeats. Our structural analyses show that ArdK, a member of this family, can form a symmetric dimer similar to that observed for KorA, yet it binds direct sequence repeats as a non-symmetric dimer. This is possible by the 180° rotation of one of the helix-turn-helix domains. We then probed and confirmed that ArdK shows affinity for an inverted repeat, which, surprisingly, is also recognized by a non-symmetrical dimer. Our results indicate that structural flexibility at different positions in the dimerization interface constrains transcription factors to bind DNA sequences with one of these two alternative DNA topologies.

PubMed: 36370103
DOI: 10.1093/nar/gkac1024

実験手法

X-RAY DIFFRACTION (3 Å)