4QJN

Crystal structure of apo nucleoid associated protein, SAV1473

4QJN の概要

• エントリーDOI: 10.2210/pdb4qjn/pdb
• 関連するPDBエントリー: 4QJU
• 分子名称: DNA-binding protein HU (2 entities in total)
• 機能のキーワード: dna condensation, dna binding, dna binding protein
• 由来する生物種: Staphylococcus aureus
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 42852.67

構造登録者

Lee, B.-J.,Kim, D.-H.,Im, H.,Yoon, H.-J. (登録日: 2014-06-04, 公開日: 2014-12-17, 最終更新日: 2023-11-08)

主引用文献

Kim, D.-H.,Im, H.,Jee, J.-G.,Jang, S.-B.,Yoon, H.-J.,Kwon, A.-R.,Kang, S.-M.,Lee, B.-J.
beta-Arm flexibility of HU from Staphylococcus aureus dictates the DNA-binding and recognition mechanism
Acta Crystallogr.,Sect.D, 70:3273-3289, 2014

PubMed Abstract: HU, one of the major nucleoid-associated proteins, interacts with the minor groove of DNA in a nonspecific manner to induce DNA bending or to stabilize bent DNA. In this study, crystal structures are reported for both free HU from Staphylococcus aureus Mu50 (SHU) and SHU bound to 21-mer dsDNA. The structures, in combination with electrophoretic mobility shift assays (EMSAs), isothermal titration calorimetry (ITC) measurements and molecular-dynamics (MD) simulations, elucidate the overall and residue-specific changes in SHU upon recognizing and binding to DNA. Firstly, structural comparison showed the flexible nature of the β-sheets of the DNA-binding domain and that the β-arms bend inwards upon complex formation, whereas the other portions are nearly unaltered. Secondly, it was found that the disruption and formation of salt bridges accompanies DNA binding. Thirdly, residue-specific free-energy analyses using the MM-PBSA method with MD simulation data suggested that the successive basic residues in the β-arms play a central role in recognizing and binding to DNA, which was confirmed by the EMSA and ITC analyses. Moreover, residue Arg55 resides in the hinge region of the flexible β-arms, exhibiting a remarkable role in their flexible nature. Fourthly, EMSAs with various DNAs revealed that SHU prefers deformable DNA. Taken together, these data suggest residue-specific roles in local shape and base readouts, which are primarily mediated by the flexible β-arms consisting of residues 50-80.

PubMed: 25478845
DOI: 10.1107/S1399004714023931

実験手法

X-RAY DIFFRACTION (2.613 Å)