A novel RNA binding surface of the TAM domain of TIP5/BAZ2A mediates epigenetic regulation of rRNA genes.
Bottom Line: Here, we show that the NMR structure of the TAM domain of TIP5 resembles the fold of the MBD domain, found in methyl-CpG binding proteins.Mutation of critical amino acids within this surface abolishes RNA binding in vitro and in vivo.Our results explain the distinct binding specificities of TAM and MBD domains to RNA and methylated DNA, respectively, and reveal structural features for the interaction of NoRC with non-coding RNA.
Affiliation: Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg D-85764, Germany Biomolecular NMR and Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München, Garching D-85747, Germany.Show MeSH
Mentions: Solution structure of the hTIP5/TAM domain. (A) Cartoon representation of the human TIP5/TAM domain. Secondary structure elements and important loops are annotated. The TAM-specific N-terminal helix and the C-terminal α/β motif are highlighted by black circles. (B) Cartoon representation of the canonical MBD domain of human MBD1 (light blue, PDB ID: 1D9N) in a comparable view as the TAM domain on the left. Secondary structure elements and the loop L1 that mediates DNA binding of the MBD1 domain are annotated. (C) Mapping of the binding surface of TIP5/TAM with pRNAmini based on NMR chemical shift perturbations (Figure 4c) onto a surface representation (left and middle panel) and a ribbon model (right) of the TIP5/TAM domain structure. Left: same view as in (a), middle and right views are rotated by 180°. Colors indicate the RNA binding surface mapped by NMR titrations (Figure 4c and d). Residues with significant chemical shift perturbation are shown in yellow, while residues that exhibit strong intensity reductions upon RNA binding are colored orange as in Figure 4c and d. (D) Electrostatic potential of the TAM domain. Vacuum electrostatics surfaces are shown blue for positive and red for negative charges for the TAM domain in the same orientations as in (c).
Affiliation: Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg D-85764, Germany Biomolecular NMR and Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München, Garching D-85747, Germany.