Figure 1. Structure-Based Sequence Alignment of SET Proteins.

The alignment includes (1) all known members of human SUV39 family: SUV39H1 (NP_003164), SUV39H2 (NP_078946), G9a (S30385), Eu-HMT1 (AAM09024), SETDB1 (NP_036564), and CLLL8 (NP_114121); (2) proteins (in bold) that have been shown to have HKMT activity from various species: N. crassa (Nc) DIM-5 (AAL35215), S. pombe (Sp) Clr4 (060016), A. thaliana (At) SUVH4 or KRYPTONITE (AAK28969), S. cerevisiae (Sc) SET1 (P38827) and SET2 (P46995), human SET7 (XP_040150) and PR-SET7 (AAL40879); (3) three bacterial SET proteins: Xylella fastidiosa (Xf) SET (AAF84287), Bradyrhizobium japonicum (Bj) SET (Q9ANB6), and Chlamydophila pneumoniae (Cp) SET (AAD19016); and (4) human EZH2 protein, which appears inactive in vitro (Rea et al., 2000). The residue number and secondary structural elements of DIM-5 (helices A–J and strands 1–17) are shown above the aligned sequences. Dashed lines indicate disordered regions. The color coding is light blue for the N terminus (residues 25–62), yellow for the pre-SET (residues 63–146), green for the SET (residues 147–236 and 248–277), magenta for the signature motifs (SET residues 237–247 and 278–285), and gray for the post-SET (residues 299–308). The amino acids highlighted are invariant (white against black) and conserved (white against gray) among almost all members of the SUV39 family. The number in parentheses indicates the number of amino acids inserted relative to the alignment. The lowercase letters above the sequences indicate the structural/functional role of the corresponding DIM-5 residues: “h” indicates intramolecular hydrophobic interaction, “n” indicates intramolecular nonhydrophobic (polar or charge) interaction, “z” indicates zinc coordination, asterisk indicates structural residue Gly or Pro, and “s” indicates surface-exposed residues potentially important for cofactor or substrate binding or catalysis. The red circles mark the residues that were mutated in this study.