An intrinsically unstructured domain in MBD2 recruits the histone deacetylase core complex of NuRD and modifies kinetics of DNA binding

Abstract

MBD2 specifically recognizes methylated DNA and recruits the NuRD chromatin remodeling complex to silence expression of the associated gene. We recently solved the structure of a coiled‐coil interaction between MBD2 and p66α that recruits the Mi2 nucleosome remodeling protein to the complex (Gnanapragasam et al., Proc Natl Acad Sci. 2011, 108:7487). In subsequent work, we have shown that a region between the methyl‐cytosine binding (MBD) and the coiled‐coil domains of MBD2 stably binds the histone deacetylase core complex of NuRD comprised by HDAC1/2, MTA1/2, and RbAp46/48. NMR and CD studies demonstrate that this region is largely unstructured even in the context of full‐length protein and while bound to methylated DNA. Immunoprecipitation studies show that the critical determinant of protein binding resides within two small molecular recognition fragments (MoRFs) that together are sufficient to recruit the core deacetylase complex. Previous analyses showed very rapid association and dissociation rates for the isolated MBD. In contrast, incorporation of the intrinsically unstructured domain reduces the association rate and markedly prolongs dissociation from methylated DNA. Therefore, this intrinsically unstructured domain functions both to recruit a large portion of the NuRD complex and stabilize interaction with methylated DNA. Supported by ACS IRG‐73‐001 (DCW) and NIH R01‐DK029902 (GDG).