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Flexible DNA bending in HU–DNA cocrystal structures
Author(s) -
Swinger Kerren K.,
Lemberg Kathryn M.,
Zhang Ying,
Rice Phoebe A.
Publication year - 2003
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1093/emboj/cdg351
Subject(s) - dna supercoil , dna , biology , nucleoid , biophysics , dihedral angle , crystallography , circular bacterial chromosome , hmg box , dna replication , dna binding protein , genetics , transcription factor , gene , physics , chemistry , hydrogen bond , escherichia coli , molecule , quantum mechanics
HU and IHF are members of a family of prokaryotic proteins that interact with the DNA minor groove in a sequence‐specific (IHF) or non‐specific (HU) manner to induce and/or stabilize DNA bending. HU plays architectural roles in replication initiation, transcription regulation and site‐specific recombination, and is associated with bacterial nucleoids. Cocrystal structures of Anabaena HU bound to DNA (1P71, 1P78, 1P51) reveal that while underlying proline intercalation and asymmetric charge neutralization mechanisms of DNA bending are similar for IHF and HU, HU stabilizes different DNA bend angles (∼105–140°). The two bend angles within a single HU complex are not coplanar, and the resulting dihedral angle is consistent with negative supercoiling. Comparison of HU–DNA and IHF–DNA structures suggests that sharper bending is correlated with longer DNA binding sites and smaller dihedral angles. An HU‐induced bend may be better modeled as a hinge, not a rigid bend. The ability to induce or stabilize varying bend angles is consistent with HU's role as an architectural cofactor in many different systems that may require differing geometries.