title: DNA-binding property of the novel DNA-binding domain STPR in FMBP-1 of the silkworm Bombyx mori.
abstract: The STPR domain is a novel DNA-binding domain composed of repeats of 23 amino-acid-long peptide found in the fibroin-modulator-binding protein-1 (FMBP-1) of the silkworm Bombyx mori. Theoretical proteins having the STPR domain are highly conserved, particularly in vertebrates, but the functions are mostly unknown. In this study, the DNA-binding property of the STPR domain in FMBP-1 was examined. Use of reagents selecting the DNA groove and an oligonucleotide in which the dA:dT pairs of the probe were replaced with dI:dC pairs in mobility shift assay demonstrated that FMBP-1 approaches DNA from the major groove. Permutation electrophoresis using probes of the same length but containing the FMBP-1-binding site at different positions showed that FMBP-1 bends DNA through its binding. To induce the sharp bend of DNA, the STPR domain alone was insufficient and the long N-terminal extending region was necessary. Moreover, the basic region extending from the N-terminus of the STPR domain stabilized the DNA binding of the STPR domain. These results suggested that DNA-binding properties of the STPR domain are affected strongly by the structure of the flanking regions in the STPR domain-containing proteins.
authors.affiliation: Department of Biological Sciences and Center for Genome Dynamics, Hokkaido University, Kita-Ku, Sapporo, Japan. takiya@rmg.hokudai.ac.jp
authors.forename: Shigeharu
authors.initials: S
authors.lastname: Takiya
authors.forename: Shin
authors.initials: S
authors.lastname: Saito
authors.forename: Takuya
authors.initials: T
authors.lastname: Yokoyama
authors.forename: Daisuke
authors.initials: D
authors.lastname: Matsumoto
authors.forename: Tomoyasu
authors.initials: T
authors.lastname: Aizawa
authors.forename: Masakatsu
authors.initials: M
authors.lastname: Kamiya
authors.forename: Makoto
authors.initials: M
authors.lastname: Demura
authors.forename: Keiichi
authors.initials: K
authors.lastname: Kawano
mesh_terms: D024506:5' Flanking Region; D000595:Amino Acid Sequence; D000818:Animals; D012831:Bombyx / Q000378:metabolism*; D017124:Conserved Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D024202:Electrophoretic Mobility Shift Assay; D019476:Insect Proteins / Q000737:chemistry / Q000378:metabolism*; D008969:Molecular Sequence Data; D050505:Mutant Proteins / Q000737:chemistry / Q000378:metabolism; D009690:Nucleic Acid Conformation; D017434:Protein Structure, Tertiary; D020449:Repetitive Sequences, Amino Acid; D016415:Sequence Alignment; D017384:Sequence Deletion
chemical_list: D004268:DNA-Binding Proteins; D019476:Insect Proteins; D050505:Mutant Proteins; D004247:DNA