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Structural properties of the DNA‐bound form of a novel tandem repeat DNA‐binding domain, STPR

Fibroin‐modulator‐binding protein 1 (FMBP‐1) is a predicted transcription factor of the silkworm fibroin gene. The DNA‐binding domain of FMBP‐1 consists of four almost perfect tandem repeats of 23 amino acids each (R1–R4), and is referred to as the score and three amino acid peptide repeat (STPR) domain. This characteristic domain is conserved in eukaryotes, but the DNA‐binding mode is not known. In this study, the structural properties of the DNA‐bound form of the STPR domain were characterized. The combined experiments indicated that the STPR domain bound to the DNA duplex with a 1:1 binding ratio. The specific DNA caused considerable changes in the thermal unfolding profile and the digestion pattern of the STPR domain. These data suggested that the domain adapts a quite rigid helix‐rich structure in the DNA‐bound state, even though it moves flexibly in the absence of DNA. Furthermore, mutual induced‐fit conformational change was also observed in DNA. Finally, we determined the DNA‐binding surface of the STPR third repeat (R3) by alanine scanning mutagenesis; a particular site, composed of hydrophobic and hydrophilic residues, was identified. Notably, the substitution of Arg‐9 in R3 with alanine residue, which is located in the middle of the surface, drastically abolished the α‐helix‐inducing and DNA‐binding abilities. From these results, we predicted the DNA‐binding mode of the STPR domain. Proteins 2008. © 2008 Wiley‐Liss, Inc.