RAG1 family members and related DNA-binding proteins containing helix-turn-helix motifs. (a) Multiple sequence alignment of the DNA-binding regions. The alignment was made using CLUSTAL W  and manually refined to reflect the secondary structural elements. Homologous DNA-binding regions from RAG1 family members, Tc3 transposase, the Hin family of recombinases, and selected homeodomain proteins are shown in the single-letter amino-acid code. For the RAG1 family the sequences are from human (hRAG1), mouse (mRAG1), rabbit (rRAG1), Xenopus (xRAG1), chicken (cRAG1), trout (tRAG1), and Fugu (fRAG1), respectively. For the Tc1 family, the sequence is from Caenorhabditis elegans Tc3 transposase (1TC3). For the Hin recombinase family, the sequences are from Salmonella typhimurium (1HCR), Salmonella abortus-equi (DNIV_SALAE), bacteriophage P1 (DNIV_BPP1), bacteriophage P7 (DNIV_BPP7), bacteriophage Mu (DNIV_BPMU), and Escherichia coli (DNIV_ECOLI). For the homeodomain family, the sequences are from Drosophila Engrailed (1HDD), Drosophila Fushi tarazu (1FTZ), Drosophila antennapedia (1AHD), Drosophila Paired (1FJL), rat Thyroid transcription factor 1 (1FTT), and Drosophila NK-2 (1VND). Amino-acid residues showing absolute identity among these proteins are shown with a blue background; those with conservative substitution are shown with a yellow background. The positions of the three α helices defined in the X-ray structures of C. elegans Tc3 transposase, Salmonella Hin recombinase, and Drosophila engrailed homeodomain are schematically represented above respective sequences. ALSCRIPT  was used to format the alignment. (b-d) Ribbon diagrams of selected helix-turn-helix motif containing protein domains bound to target DNA. The α-carbon backbone of the protein is depicted in blue and the DNA as a yellow ribbon, respectively. Helices and loop regions are as defined in (a). The ribbon diagram was generated using the Visual Molecular Dynamics program  with the atomic coordinates from (b) C.elegans Tc3 transposase (PDB  entry 1Tc3), (c) Salmonella Hin recombinase (PDB entry 1HCR), and (d) Drosophila engrailed homeodomain (PDB entry 1HDD).
Banerjee-Basu and Baxevanis Genome Biology 2002 3:interactions1004.1 doi:10.1186/gb-2002-3-8-interactions1004