ABSTRACT
Nucleosome remodeling and deacetylation (NuRD) complexes are co-transcriptional regulators implicated in differentiation, development, and diseases. Methyl-CpG binding domain (MBD) proteins play an essential role in recruitment of NuRD complexes to their target sites in chromatin. The related SHREC complex in fission yeast drives transcriptional gene silencing in heterochromatin through cooperation with HP1 proteins. How remodeler and histone deacetylase (HDAC) cooperate within NuRD complexes remains unresolved. We determined that in SHREC the two modules occupy distant sites on the scaffold protein Clr1 and that repressive activity of SHREC can be modulated by the expression level of the HDAC-associated Clr1 domain alone. Moreover, the crystal structure of Clr2 reveals an MBD-like domain mediating recruitment of the HDAC module to heterochromatin. Thus, SHREC bi-functionality is organized in two separate modules with separate recruitment mechanisms, which work together to elicit transcriptional silencing at heterochromatic loci.
Subject(s)
Chromatin Assembly and Disassembly , Gene Silencing , Heterochromatin/metabolism , Mi-2 Nucleosome Remodeling and Deacetylase Complex/metabolism , Protein Processing, Post-Translational , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/enzymology , Acetylation , Binding Sites , CpG Islands , DNA, Fungal/metabolism , Gene Expression Regulation, Fungal , Heterochromatin/chemistry , Heterochromatin/genetics , Mi-2 Nucleosome Remodeling and Deacetylase Complex/chemistry , Mi-2 Nucleosome Remodeling and Deacetylase Complex/genetics , Models, Molecular , Nucleosomes/enzymology , Nucleosomes/genetics , Protein Binding , Protein Conformation , Protein Interaction Domains and Motifs , RNA, Fungal/metabolism , Schizosaccharomyces/genetics , Schizosaccharomyces pombe Proteins/chemistry , Schizosaccharomyces pombe Proteins/genetics , Structure-Activity Relationship , Transcription Factors/genetics , Transcription Factors/metabolism , Transcription, GeneticABSTRACT
IP3-3K [Ins(1,4,5)P3 3-kinase] is a key enzyme that catalyses the synthesis of Ins(1,3,4,5)P4, using Ins(1,4,5)P3 and ATP as substrates. Both inositides, substrate and product, present crucial roles in the cell. Ins(1,4,5)P3 is a key point in Ca2+ metabolism that promotes Ca2+ release from intracellular stores and together with Ins(1,3,4,5)P4 regulates Ca2+ homoeostasis. In addition, Ins(1,3,4,5)P4 is involved in immune cell development. It has been proved that Ca2+/CaM (calmodulin) regulates the activity of IP3-3K, via direct interaction between both enzymes. Although we have extensive structural knowledge of the kinase domains of the three IP3-3K isoforms, no structural information is available about the interaction between IP3-3K and Ca2+/CaM. In the present paper we describe the crystal structure of the complex between human Ca2+/CaM and the CaM-binding region of human IP3-3K isoform A (residues 158-183) and propose a model for a complex including the kinase domain. The structure obtained allowed us to identify all of the key residues involved in the interaction, which have been evaluated by site-directed mutagenesis, pull-down and fluorescence anisotropy experiments. The results allowed the identification of a new CaM-binding motif, expanding our knowledge about how CaM interacts with its partners.
