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Flexible DNA bending in HU-DNA cocrystal structures.
Kerren K Swinger1, Kathryn M Lemberg, Ying Zhang
1Department of Biochemistry and Molecular Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
The EMBO Journal
|July 11, 2003
Summary
Bacterial HU protein induces and stabilizes DNA bending, acting as a flexible hinge rather than a rigid structure. This architectural role is crucial for various DNA processes, adapting to different geometric requirements.
Area of Science:
- Structural biology
- Molecular biology
- Biochemistry
Background:
- HU and Integration Host Factor (IHF) are prokaryotic proteins interacting with DNA.
- They modulate DNA structure through bending, essential for various cellular processes.
- HU is involved in replication, transcription, and recombination, and is associated with nucleoids.
Purpose of the Study:
- To investigate the DNA bending mechanisms and structural roles of HU protein.
- To compare HU-DNA interactions with IHF-DNA interactions.
- To understand how HU stabilizes varying DNA bend angles.
Main Methods:
- Cocrystallography of Anabaena HU bound to DNA.
- Structural analysis of HU-DNA complexes (PDB IDs: 1P71, 1P78, 1P51).
- Comparison with existing IHF-DNA structures.
Main Results:
- HU stabilizes DNA bend angles between approximately 105-140 degrees.
- The two bend angles within an HU complex are non-coplanar, suggesting a role in negative supercoiling.
- Sharper DNA bending correlates with longer binding sites and smaller dihedral angles.
- HU-induced DNA bends are better modeled as flexible hinges.
Conclusions:
- HU acts as a versatile architectural cofactor, inducing and stabilizing DNA bends with adaptable geometries.
- The non-coplanar bends and dihedral angles are consistent with HU's role in managing DNA supercoiling.
- HU's flexibility in bending allows it to function in diverse DNA-related systems requiring specific geometries.