5d23 | pdb_00005d23

The crystal structure of STPR from Bombyx mori in complex with 13-bp DNA derived from the +290 site of fibroin gene

spinqualitylabelsall models 5d23, resolution 1.95Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5d23 is a 2 chain structure with sequence from Bombyx mori and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.95Å Ligands: MSE Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q5FBS0_BOMMO Publication Abstract from PubMed 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 alpha-helices that run along the major groove of DNA. Structural analyses combined with binding assays indicate BmSTPR prefers the AT-rich sequences, with each alpha-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 alpha-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. Structures of an all-alpha protein running along the DNA major groove.,Yu LY, Cheng W, Zhou K, Li WF, Yu HM, Gao X, Shen X, Wu Q, Chen Y, Zhou CZ Nucleic Acids Res. 2016 May 5;44(8):3936-45. doi: 10.1093/nar/gkw133. Epub 2016, Mar 2. PMID:26939889 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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