title: Entrapment of DNA in an intersubunit tunnel system of a single-stranded DNA-binding protein.
abstract: Instead of a classical single-stranded deoxyribonuleic acid (DNA)-binding protein (SSB), some hyperthermophilic crenarchaea harbor a non-canonical SSB termed ThermoDBP. Two related but poorly characterized groups of proteins, which share the ThermoDBP N-terminal DNA-binding domain, have a broader phylogenetic distribution and co-exist with ThermoDBPs and/or other SSBs. We have investigated the nucleic acid binding properties and crystal structures of representatives of these groups of ThermoDBP-related proteins (ThermoDBP-RPs) 1 and 2. ThermoDBP-RP 1 and 2 oligomerize by different mechanisms and only ThermoDBP-RP2 exhibits strong single-stranded DNA affinity in vitro. A crystal structure of ThermoDBP-RP2 in complex with DNA reveals how the NTD common to ThermoDBPs and ThermoDBP-RPs can contact the nucleic acid in a manner that allows a symmetric homotetrameric protein complex to bind single-stranded DNA molecules asymmetrically. While single-stranded DNA wraps around the surface or binds along channels of previously investigated SSBs, it traverses an internal, intersubunit tunnel system of a ThermoDBP-RP2 tetramer. Our results indicate that some archaea have acquired special SSBs for genome maintenance in particularly challenging environments.
authors.affiliation: Freie Universität Berlin, Fachbereich Biologie, Chemie, Pharmazie, Institut für Chemie und Biochemie, AG Strukturbiochemie, Takustr. 6, 14195 Berlin, Germany Max-Planck-Institute for Biophysical Chemistry, Department of Cellular Biochemistry, Am Fassberg 11, 37077 Göttingen, Germany.
authors.forename: Homa
authors.initials: H
authors.lastname: Ghalei
authors.affiliation: Freie Universität Berlin, Fachbereich Biologie, Chemie, Pharmazie, Institut für Chemie und Biochemie, AG Strukturbiochemie, Takustr. 6, 14195 Berlin, Germany.
authors.forename: Holger
authors.initials: H
authors.lastname: von Moeller
authors.affiliation: Freie Universität Berlin, Fachbereich Biologie, Chemie, Pharmazie, Institut für Chemie und Biochemie, AG Strukturbiochemie, Takustr. 6, 14195 Berlin, Germany.
authors.forename: Detlef
authors.initials: D
authors.lastname: Eppers
authors.affiliation: Gene Center, Department of Biochemistry and Center of integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Sohmen
authors.affiliation: Gene Center, Department of Biochemistry and Center of integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany.
authors.forename: Daniel N
authors.initials: DN
authors.lastname: Wilson
authors.affiliation: Freie Universität Berlin, Fachbereich Biologie, Chemie, Pharmazie, Institut für Chemie und Biochemie, AG Strukturbiochemie, Takustr. 6, 14195 Berlin, Germany.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Loll
authors.affiliation: Freie Universität Berlin, Fachbereich Biologie, Chemie, Pharmazie, Institut für Chemie und Biochemie, AG Strukturbiochemie, Takustr. 6, 14195 Berlin, Germany mwahl@zedat.fu-berlin.de.
authors.forename: Markus C
authors.initials: MC
authors.lastname: Wahl
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D011485:Protein Binding; D020027:Pyrococcus furiosus; D012313:RNA / Q000378:metabolism
chemical_list: D019843:Archaeal Proteins; D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins; D012313:RNA; D004247:DNA
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