4QJU

Crystal structure of DNA-bound nucleoid associated protein, SAV1473

Summary for 4QJU

• Entry DOI: 10.2210/pdb4qju/pdb
• Related: 4QJN
• Descriptor: DNA-binding protein HU, DNA (5'-D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3') (3 entities in total)
• Functional Keywords: dna condensation, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Staphylococcus aureus; More
• Total number of polymer chains: 4
• Total formula weight: 34184.60

Authors

Lee, B.-J.,Kim, D.-H.,Im, H.,Yoon, H.-J. (deposition date: 2014-06-04, release date: 2014-12-17, Last modification date: 2023-11-08)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.16 Å)