The SAF-box domain of chromatin protein DEK

• Published in: Nucleic acids research 2005-01, Vol.33 (3), p.1101-1110
• Main Authors: Böhm, Friederike, Kappes, Ferdinand, Scholten, Ingo, Richter, Nicole, Matsuo, Hiroshi, Knippers, Rolf, Waldmann, Tanja
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Binding Sites; Chromatin - metabolism; Chromosomal Proteins, Non-Histone - chemistry; Chromosomal Proteins, Non-Histone - metabolism; DNA - metabolism; DNA, Cruciform - metabolism; DNA, Superhelical - chemistry; Humans; Molecular Sequence Data; Oncogene Proteins - chemistry; Oncogene Proteins - metabolism; Peptides - metabolism; Poly-ADP-Ribose Binding Proteins; Protein Structure, Tertiary
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gki258

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.