Structural evidence for protein-protein interaction between the non-canonical methyl-CpG-binding domain of SETDB proteins and C11orf46.

SETDB1 and SETDB2 mediate trimethylation of histone H3 lysine 9 (H3K9), an epigenetic hallmark of repressive chromatin. They contain a non-canonical methyl-CpG-binding domain (MBD) and bifurcated SET domain, implying interplay between H3K9 trimethylation and DNA methylation in SETDB functions. Here, we report the crystal structure of human SETDB2 MBD bound to the cysteine-rich domain of a zinc-binding protein, C11orf46. SETDB2 MBD comprises the conserved MBD core and a unique N-terminal extension. Although the MBD core has the conserved basic concave surface for DNA binding, it utilizes it for recognition of the cysteine-rich domain of C11orf46. This interaction involves the conserved arginine finger motif and the unique N-terminal extension of SETDB2 MBD, with a contribution from intermolecular β-sheet formation. Thus, the non-canonical MBD of SETDB1/2 seems to have lost methylated DNA-binding ability but gained a protein-protein interaction surface. Our findings provide insight into the molecular assembly of SETDB-associated repression complexes. [Display omitted] • SETDB1/2 directly interacts with C11orf46 CRD through their non-canonical MBDs • Crystal structure of the SETDB2 MBD–C11orf46 CRD complex at 1.82 Å resolution • Conserved and divergent characteristics of the non-canonical MBD of SETDB proteins • The zinc-binding motifs in C11orf46 CRD contribute to maintaining its core fold C11orf46 has been identified in SETDB-associated repression complexes. Mahana et al. demonstrate that the non-canonical MBD of SETDB2, despite its conserved MBD architecture, mediates a protein-protein interaction with C11orf46 CRD rather than methylated DNA binding. This finding highlights the diverse functional roles of MBDs in transcriptional repression. [ABSTRACT FROM AUTHOR]