Structures of an all-α protein running along the DNA major groove

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.

Figure 1.

Structure of BmSTPR. (A) Domain organization of FMBP-1. (B) Sequence alignment of the four repeats of BmSTPR. The highly conserved residues involved in DNA binding are labelled with blue pentangles. (C) Crystal structure of BmSTPR in complex with the 13-bp DNA. Repeats R2 to R4 are shown as cylinders and coloured in cyan, yellow and purple, respectively. The coding and noncoding strands of the 13-bp DNA are shown as green and orange, respectively. The detailed interactions that stabilize the repeats R3 and R4 of BmSTPR are zoomed-in at the right panel. The involved residues are labelled and shown as sticks.

Figure 2.

The tandem interactions between BmSTPR and 13-bp DNA. (A) A diagram of BmSTPR interacting with DNA. Residues from R2 to R4 are coloured as their located repeat. Water molecules are donated as open circles labelled with the letter ‘W’. The contacted base groups are displayed as light orange and green, respectively. (B) Cartoon representation of the contacts between R2 to R4 and corresponding nucleotides. The involved nucleotides and residues are labelled and shown as sticks. Water molecules are shown as red spheres.

Figure 3.

The favoured 4-bp repetitive unit binding to BmSTPR. (A) A context-dependent consensus generated by the first-order Markov chains algorithm. (B) The correlation analysis of the context-dependent consensus.

Figure 4.

The structure of BmSTPR in complex with 18-bp DNA containing four repeats of 5′-atac-3′. (A) Cartoon representation of BmSTPR in complex with 18-bp DNA. The DNA strands and repeats of BmSTPR adopt the same colour coding as Figure 1C, in addition to R1 coloured in red. (B) Cartoon representation of the contacts between R1 and corresponding nucleotides in the 18-bp DNA complexed structure. The involved nucleotides and residues are labelled and shown as sticks. The water molecules are indicated as red spheres and marked with the letter ‘W’. (C) A diagram of the interactions between BmSTPR and 18-bp DNA.

Figure 5.

Multiple-sequence alignment of BmSTPR against its homologs with the programs Cobalt (46) and Espript (47). The secondary structural elements of BmSTPR are displayed at the top. The three conserved residues such as Glu1, Arg9 and Thr/Ser2 in each repeat are labelled with red stars. The STPR domains are from the following sequences (NCBI accession numbers in parentheses): B. mori FMBP-1 (NP_001036969.1), H. sapiens Zinc finger protein 821 isoform 2 (NP_060000.1), D. rerio predicted Zinc finger protein 821-like isoform X1 (XP_005169107.1), Drosophila-1 CG14440 isoform A (NP_572343.1), Drosophila-2 CG14442 isoform A (NP_572342.1), C. elegans protein C05D11.13 (NP_498414.1) and P. patens predicted protein (XP_001767050.1). All STPRs cover the four repeats from R1 to R4, except Drosophila-2 covers repeats R3–R6.