Crystal Structure and Functional Analysis of the Histone Methyltransferase SET7/9
Crystal Structure and Functional Analysis of the Histone Methyltransferase SET7/9 actively transcribed genes are thought to be structurally clustered into regions having a more open, or less compact, conformation of chromatin (somal region adopts a heterochromatic or euchromatic 1 Structural Biology Group state is determined, at least in part, by the patterns of National Institute for Medical Research posttranscriptional modification of the N-terminal tails The Ridgeway, Mill Hill of the core
... stones (Strahl and Allis, 2000; Zhang and London NW7 1AA Reinberg, 2001) that include acetylation, phosphoryla-United Kingdom tion, and methylation. While acetylation of specific lysine 2 Department of Chemistry residues is associated with transcriptional activation Krebs Institute (Grunstein, 1997), lysine methylation seems to be in-University of Sheffield volved in both activation and repression of transcription Sheffield S3 7HF (Litt et al., 2001; Noma et al., 2001), depending on the United Kingdom context of the modification. The combinatorial nature of these histone modifications has been proposed to represent a "histone code" that acts in addition to the Summary underlying genetic code (Strahl and Allis, 2000; Turner, 2000). Methylation of lysine residues in the N-terminal tails Although methylation of histone lysine residues was of histones is thought to represent an important comreported as long ago as 1964 (Murray, 1964), only reponent of the mechanism that regulates chromatin cently has the class of enzymes responsible for this structure. The evolutionarily conserved SET domain modification and their functional significance been idenoccurs in most proteins known to possess histone tified (Rea et al., 2000). Rea et al. first demonstrated the lysine methyltransferase activity. We present here the connection between a domain widely distributed among crystal structure of a large fragment of human SET7/9 proteins connected with chromatin remodeling in higher that contains a N-terminal ␤-sheet domain as well as organisms and a group of plant enzymes with methylthe conserved SET domain. Mutagenesis identifies transferase activity. They were able to demonstrate that two residues in the C terminus of the protein that the human homolog of the suppressor of variegation appear essential for catalytic activity toward lysine-4 enzyme, SUV39H1, carried out specific methylation of of histone H3. Furthermore, we show how the cofactor lysine 9 on the N terminus of histone H3. This work also AdoMet binds to this domain and present biochemical showed that although the catalytic core of this protein data supporting the role of invariant residues in catalywas located within the so-called SET domain (Jones sis, binding of AdoMet, and interactions with the pepand Gelbart, 1993; Tschiersch et al., 1994), both N-and tide substrate. C-terminal flanking domains were also required for histone methyltransferase (HMTase) activity. It has been Introduction estimated that there are seven to ten gene families in mammals that contain SET domains (Lachner and Jen-In eukaryotes, nuclear DNA is packaged with specific uwein, 2002). These domains invariably occur within a proteins to form chromatin. At the lowest level of chrolarger protein and are mostly frequently located near mosome organization is the nucleosome, consisting of the C terminus. Sequence alignments have revealed two a core of an octamer of histones (two heterodimers of regions of strong sequence conservation within the SET H2A/H2B and a tetramer of H3/H4), around which 146 domain (Rea et al., 2000) . These motifs, 320 H(x) 2 NHSC 326 base pairs of negatively supercoiled DNA are wound and 358 GEEL(x) 3 Y 365 in the human SUV39H1, both occur (Luger et al., 1997) . The N-terminal tails of the histones in the C-terminal half of the SET domain and, together protrude from the core and are subject to posttranslawith mutational data, were interpreted as defining an tional modifications. Nucleosomes are the building important catalytic site. Also apparent from phylogeblocks for the formation of successively higher levels of netic analysis is the fact that, although apparently essenchromosome organization and compactness. At mitotial for HMTase activity, the domains, which occur immesis, chromosomes adopt their most compact state, and diately adjacent to the N and C termini of the SET subsequently, heterochromatic regions remain comdomain, vary considerably amongst the many SET-conpacted during interphase while euchromatic regions betaining proteins (Roguev et al., 2001) . come more dispersed (Dillon and Festenstein, 2002) . There are at least two ways in which HMTase activity Processes requiring some degree of access to the geis thought to alter chromatin structure and gene expresnetic information, such as DNA replication, repair, and sion patterns. First, methylation of lysine 9 on histone transcription, are restrained by the degree of compact-H3 has been shown to generate a high-affinity binding ness of the chromatin (Wolffe, 1998). In general terms, site for HP1 proteins (Bannister et al., 2001; Lachner et al., 2001; Nakayama et al., 2001). The latter constitute a family of heterochromatic adaptor molecules with 3 Correspondence: firstname.lastname@example.org 4 These authors contributed equally to this work. roles in gene silencing and higher-order chromatin as-Cell 106 Zhang, Y., and Reinberg, D. (2001). Transcription regulation by his-Masino, L., Martin, S.R., and Bayley, P.M. (2000). Ligand binding tone methylation: interplay between different covalent modifications and thermodynamic stability of a multidomain protein, calmodulin. of the core histone tails. Genes Dev. 15, 2343-2360. Protein Sci. 9, 1519-1529. Murray, K. (1964). The occurrence of ⑀-N-methyl lysine in histones. Accession Numbers Biochemistry 3, 10-15. The coordinates of Set 7/9 have been deposited in the Protein Data (2001). Role of histone H3 lysine 9 methylation in epigenetic control Bank with the code 1h3i. of heterochromatin assembly. Science 292, 110-113. Nishioka, K., Chuikov, S., Sarma, K., Erdjument-Bromage, H., Allis, C.D., Tempst, P., and Reinberg, D. (2002a). Set9, a novel histone H3 methyltransferase that facilitates transcription by precluding histone tail modifications required for heterochromatin formation. Genes Dev. 16, 479-489.