title: The solution structure and DNA-binding properties of the cold-shock domain of the human Y-box protein YB-1.
abstract: The human Y-box protein 1 (YB-1) is a member of the Y-box protein family, a class of proteins involved in transcriptional and translational regulation of a wide range of genes. Here, we report the solution structure of the cold-shock domain (CSD) of YB-1, which is thought to be responsible for nucleic acid binding. It is the first structure solved of a eukaryotic member of the cold-shock protein family and consists of a closed five-stranded anti-parallel beta-barrel capped by a long flexible loop. The structure of CSD is similar to the OB-fold and a comparison with bacterial cold-shock proteins shows that its structural properties are conserved from bacteria to man. Our data suggest the presence of a DNA-binding site consisting of a patch of positively charged and aromatic residues on the surface of the beta-barrel. Further, it is shown that CSD, which has a preference for binding single-stranded pyrimidine-rich sequences, binds weakly and hardly specifically to DNA. Binding affinities reported for intact YB-1 indicate that domains other than the CSD play a role in DNA binding of YB-1.
authors.affiliation: NSR Center for Molecular Structure, Design and Synthesis, Laboratory of Biophysical Chemistry, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands.
authors.forename: Cathelijne P A M
authors.initials: CP
authors.lastname: Kloks
authors.forename: Christian A E M
authors.initials: CA
authors.lastname: Spronk
authors.forename: Edwin
authors.initials: E
authors.lastname: Lasonder
authors.forename: Astrid
authors.initials: A
authors.lastname: Hoffmann
authors.forename: Geerten W
authors.initials: GW
authors.lastname: Vuister
authors.forename: Stephan
authors.initials: S
authors.lastname: Grzesiek
authors.forename: Cornelis W
authors.initials: CW
authors.lastname: Hilbers
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D022762:CCAAT-Enhancer-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D003080:Cold Temperature; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D051839:NFI Transcription Factors; D019906:Nuclear Magnetic Resonance, Biomolecular; D009687:Nuclear Proteins; D009838:Oligodeoxyribonucleotides / Q000235:genetics / Q000378:metabolism; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D020218:Response Elements / Q000235:genetics; D016415:Sequence Alignment; D012996:Solutions; D020349:Surface Plasmon Resonance; D014157:Transcription Factors; D051840:Y-Box-Binding Protein 1
chemical_list: D022762:CCAAT-Enhancer-Binding Proteins; D004268:DNA-Binding Proteins; D051839:NFI Transcription Factors; D009687:Nuclear Proteins; D009838:Oligodeoxyribonucleotides; D012996:Solutions; D014157:Transcription Factors; D051840:Y-Box-Binding Protein 1; C070856:YBX1 protein, human; D004247:DNA