EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR.
ジャーナル・号・ページ	Nucleic Acids Res, Vol. 51, Issue 15, Page 8237-8254, Year 2023
掲載日	2023年8月25日
著者	Ida Freda / Cécile Exertier / Anna Barile / Antonio Chaves-Sanjuan / Mirella Vivoli Vega / Michail N Isupov / Nicholas J Harmer / Elena Gugole / Paolo Swuec / Martino Bolognesi / Anita Scipioni / Carmelinda Savino / Martino Luigi Di Salvo / Roberto Contestabile / Beatrice Vallone / Angela Tramonti / Linda Celeste Montemiglio /
PubMed 要旨	Specificity in protein-DNA recognition arises from the synergy of several factors that stem from the structural and chemical signatures encoded within the targeted DNA molecule. Here, we deciphered ...Specificity in protein-DNA recognition arises from the synergy of several factors that stem from the structural and chemical signatures encoded within the targeted DNA molecule. Here, we deciphered the nature of the interactions driving DNA recognition and binding by the bacterial transcription factor PdxR, a member of the MocR family responsible for the regulation of pyridoxal 5'-phosphate (PLP) biosynthesis. Single particle cryo-EM performed on the PLP-PdxR bound to its target DNA enabled the isolation of three conformers of the complex, which may be considered as snapshots of the binding process. Moreover, the resolution of an apo-PdxR crystallographic structure provided a detailed description of the transition of the effector domain to the holo-PdxR form triggered by the binding of the PLP effector molecule. Binding analyses of mutated DNA sequences using both wild type and PdxR variants revealed a central role of electrostatic interactions and of the intrinsic asymmetric bending of the DNA in allosterically guiding the holo-PdxR-DNA recognition process, from the first encounter through the fully bound state. Our results detail the structure and dynamics of the PdxR-DNA complex, clarifying the mechanism governing the DNA-binding mode of the holo-PdxR and the regulation features of the MocR family of transcription factors.
リンク	Nucleic Acids Res / PubMed:37378428 / PubMed Central
手法	EM (単粒子) / X線回折
解像度	2.8 - 4.0 Å
構造データ	14778 7zla EMDB-14778, PDB-7zla: Cryo-EM structure of holo-PdxR from Bacillus clausii bound to its target DNA in the half-closed conformation 手法: EM (単粒子) / 解像度: 3.99 Å 14801 7zn5 EMDB-14801: Cryo-EM structure of holo-PdxR from Bacillus clausii bound to its target DNA in the closed conformation, C2 symmetry PDB-7zn5: Cryo-EM structure of holo-PdxR from Bacillus clausii bound to its target DNA in the closed conformation, C2 symmetry. 手法: EM (単粒子) / 解像度: 3.7 Å 14852 7zpa EMDB-14852, PDB-7zpa: Cryo-EM structure of holo-PdxR from Bacillus clausii bound to its target DNA in the closed conformation, C1 symmetry 手法: EM (単粒子) / 解像度: 3.9 Å 14960 7zth EMDB-14960, PDB-7zth: Cryo-EM structure of holo-PdxR from Bacillus clausii bound to its target DNA in the open conformation 手法: EM (単粒子) / 解像度: 4.0 Å PDB-7pq9: Crystal structure of Bacillus clausii pdxR at 2.8 Angstroms resolution 手法: X-RAY DIFFRACTION / 解像度: 2.8 Å
化合物	ChemComp-CA: Unknown entry / カルシウムジカチオン ChemComp-CL: Unknown entry / クロリド / 塩化物 ChemComp-PGE: TRIETHYLENE GLYCOL / トリエチレングリコ-ル / ポリエチレングリコール ChemComp-EDO: 1,2-ETHANEDIOL / エチレングリコ-ル / エチレングリコール ChemComp-PEG: DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル / ジエチレングリコール ChemComp-P6G: HEXAETHYLENE GLYCOL / ヘキサエチレングリコ-ル / 沈殿剤YM / ポリエチレングリコール ChemComp-HOH*: WATER / 水
由来	alkalihalobacillus clausii (バクテリア)
キーワード	DNA BINDING PROTEIN (DNA結合タンパク質) / Bacillus clausii; MocR; PdxR; pyridoxal 5'-phosphate biosynthesis; transcriptional regulation; apo / transcription factor (転写因子) / PLP-binding protein / domain-swap homodimer