title: Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein.
abstract: The crystal structure of TrmBL2 from the archaeon Pyrococcus furiosus shows an association of two pseudosymmetric dimers. The dimers follow the prototypical design of known bacterial repressors with two helix-turn-helix (HTH) domains binding to successive major grooves of the DNA. However, in TrmBL2, the two dimers are arranged at a mutual displacement of approximately 2bp so that they associate with the DNA along the double-helical axis at an angle of approximately 80°. While the deoxyribose phosphate groups of the double-stranded DNA (dsDNA) used for co-crystallization are clearly seen in the electron density map, most of the nucleobases are averaged out. Refinement required to assume a superposition of at least three mutually displaced dsDNAs. The HTH domains interact primarily with the deoxyribose phosphate groups and polar interactions with the nucleobases are almost absent. This hitherto unseen mode of DNA binding by TrmBL2 seems to arise from nonoptimal protein-DNA contacts made by its four HTH domains resulting in a low-affinity, nonspecific binding to DNA.
authors: University of Konstanz Department of Biology, Universitätsstrasse 10, 78456 Konstanz, Germany.
authors: Misbha Ud Din
authors: MUD
authors: Ahmad
authors: University Regensburg Lehrstuhl für Mikrobiologie, Universitätsstrasse 31, 93053 Regensburg, Germany.
authors: Ingrid
authors: I
authors: Waege
authors: University Regensburg Lehrstuhl für Mikrobiologie, Universitätsstrasse 31, 93053 Regensburg, Germany.
authors: Winfried
authors: W
authors: Hausner
authors: University Regensburg Lehrstuhl für Mikrobiologie, Universitätsstrasse 31, 93053 Regensburg, Germany.
authors: Michael
authors: M
authors: Thomm
authors: University of Konstanz Department of Biology, Universitätsstrasse 10, 78456 Konstanz, Germany.
authors: Winfried
authors: W
authors: Boos
authors: University of Konstanz Department of Biology, Universitätsstrasse 10, 78456 Konstanz, Germany.
authors: Kay
authors: K
authors: Diederichs
authors: University of Konstanz Department of Biology, Universitätsstrasse 10, 78456 Konstanz, Germany. Electronic address: wolfram.welte@uni-konstanz.de.
authors: Wolfram
authors: W
authors: Welte
mesh_terms: D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000378:metabolism / Q000648:ultrastructure*; D002843:Chromatin / Q000378:metabolism; D018360:Crystallography, X-Ray; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism / Q000648:ultrastructure*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D020027:Pyrococcus furiosus / Q000235:genetics / Q000378:metabolism*; D016415:Sequence Alignment
chemical_list: D019843:Archaeal Proteins; D002843:Chromatin; D004268:DNA-Binding Proteins; D004247:DNA
keywords: Archaea; TrmBL2; chromatin protein; nonspecific DNA binding; protein–DNA complex