title: The SAF-box domain of chromatin protein DEK.
abstract: DEK is an abundant chromatin protein in metazoans reaching copy numbers of several millions/nucleus. Previous work has shown that human DEK, a protein of 375 amino acids, has two functional DNA-binding domains, of which one resides in a central part of the molecule and contains sequences corresponding to the scaffold attachment factor-box (SAF-box) domain as found in a growing number of nuclear proteins. Isolated SAF-box peptides (amino acids 137-187) bind weakly to DNA in solution, but when many SAF-box peptides are brought into close proximity on the surface of Sephadex beads, cooperative effects lead to a high affinity to DNA. Furthermore, a peptide (amino acids 87-187) that includes a sequence on the N-terminal side of the SAF-box binds efficiently to DNA. This peptide prefers four-way junction DNA over straight DNA and induces supercoils in relaxed circular DNA just like the full-length DEK. Interestingly, however, the 87-187 amino acid peptide introduces negative supercoils in contrast to the full-length DEK, which is known to introduce positive supercoils. We found that two adjacent regions (amino acids 68-87 and 187-250) are necessary for the formation of positive supercoils. Our data contribute to the ongoing characterization of the abundant and ubiquitous DEK chromatin protein.
authors.affiliation: Department of Biology, University of Konstanz 78457 Konstanz, Germany.
authors.forename: Friederike
authors.initials: F
authors.lastname: Böhm
authors.forename: Ferdinand
authors.initials: F
authors.lastname: Kappes
authors.forename: Ingo
authors.initials: I
authors.lastname: Scholten
authors.forename: Nicole
authors.initials: N
authors.lastname: Richter
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Matsuo
authors.forename: Rolf
authors.initials: R
authors.lastname: Knippers
authors.forename: Tanja
authors.initials: T
authors.lastname: Waldmann
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D002843:Chromatin / Q000378:metabolism; D002868:Chromosomal Proteins, Non-Histone / Q000737:chemistry* / Q000378:metabolism; D004247:DNA / Q000378:metabolism; D045566:DNA, Cruciform / Q000378:metabolism; D004278:DNA, Superhelical / Q000737:chemistry; D006801:Humans; D008969:Molecular Sequence Data; D015513:Oncogene Proteins / Q000737:chemistry* / Q000378:metabolism; D010455:Peptides / Q000378:metabolism; D000075223:Poly-ADP-Ribose Binding Proteins; D017434:Protein Structure, Tertiary
chemical_list: D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D045566:DNA, Cruciform; D004278:DNA, Superhelical; C084738:DEK protein, human; D015513:Oncogene Proteins; D010455:Peptides; D000075223:Poly-ADP-Ribose Binding Proteins; D004247:DNA
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