5D2S

Crystal structure of STPR from Bombyx mori in complex with 18-bp DNA containing four repetitive units of ATAC

5D2S の概要

• エントリーDOI: 10.2210/pdb5d2s/pdb
• 関連するPDBエントリー: 5D23 5D2Q
• 分子名称: Fibroin-modulator-binding protein-1, DNA (36-MER) (3 entities in total)
• 機能のキーワード: protein-dna complex, all a-helix, dna major groove binding, transcription-dna complex, transcription/dna
• 由来する生物種: Bombyx mori (Silk moth); 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 22886.67

構造登録者

Cheng, W. (登録日: 2015-08-06, 公開日: 2016-03-23, 最終更新日: 2024-03-20)

主引用文献

Yu, L.Y.,Cheng, W.,Zhou, K.,Li, W.F.,Yu, H.M.,Gao, X.,Shen, X.,Wu, Q.,Chen, Y.,Zhou, C.Z.
Structures of an all-alpha protein running along the DNA major groove.
Nucleic Acids Res., 2016

PubMed Abstract: Despite over 3300 protein-DNA complex structures have been reported in the past decades, there remain some unknown recognition patterns between protein and target DNA. The silkgland-specific transcription factor FMBP-1 from the silkworm Bombyx mori contains a unique DNA-binding domain of four tandem STPRs, namely the score and three amino acid peptide repeats. Here we report three structures of this STPR domain (termed BmSTPR) in complex with DNA of various lengths. In the presence of target DNA, BmSTPR adopts a zig-zag structure of three or four tandem α-helices that run along the major groove of DNA. Structural analyses combined with binding assays indicate BmSTPR prefers the AT-rich sequences, with each α-helix covering a DNA sequence of 4 bp. The successive AT-rich DNAs adopt a wider major groove, which is in complementary in shape and size to the tandem α-helices of BmSTPR. Substitutions of DNA sequences and affinity comparison further prove that BmSTPR recognizes the major groove mainly via shape readout. Multiple-sequence alignment suggests this unique DNA-binding pattern should be highly conserved for the STPR domain containing proteins which are widespread in animals. Together, our findings provide structural insights into the specific interactions between a novel DNA-binding protein and a unique deformed B-DNA.

PubMed: 26939889
DOI: 10.1093/nar/gkw133

実験手法

X-RAY DIFFRACTION (2.2 Å)