Structure of the 30-kDa Sin3-associated protein (SAP30) in complex with the mammalian Sin3A corepressor and its role in nucleic acid binding

J Biol Chem. 2011 Aug 5;286(31):27814-24. doi: 10.1074/jbc.M111.252494. Epub 2011 Jun 15.


The ∼2-megadalton evolutionarily conserved histone deacetylase-associated Rpd3L/Sin3L complex plays critical roles in altering the histone code and repressing transcription of a broad range of genes involved in many aspects of cellular physiology. Targeting of this complex to specific regions of the genome is presumed to rely on interactions involving one or more of at least 10 distinct subunits in the complex. Here we describe the solution structure of the complex formed by the interacting domains of two constitutively associated subunits, mSin3A and SAP30. The mSin3A paired amphipathic helix 3 (PAH3) domain in the complex adopts the left-handed four-helix bundle structure characteristic of PAH domains. The SAP30 Sin3 interaction domain (SID) binds to PAH3 via a tripartite structural motif, including a C-terminal helix that targets the canonical PAH hydrophobic cleft while two other helices and an N-terminal extension target a discrete surface formed largely by the PAH3 α2, α3, and α3' helices. The protein-protein interface is extensive (∼1400 Å(2)), accounting for the high affinity of the interaction and the constitutive association of the SAP30 subunit with the Rpd3L/Sin3L complex. We further show using NMR that the mSin3A PAH3-SAP30 SID complex can bind to nucleic acids, hinting at a role for a nucleolar localization sequence in the SID αA helix in targeting the Rpd3L/Sin3L complex for silencing ribosomal RNA genes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Chromatography, High Pressure Liquid
  • DNA Primers
  • Histone Deacetylases / chemistry
  • Histone Deacetylases / metabolism
  • Histone Deacetylases / physiology*
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular
  • Nucleic Acids / metabolism*
  • Protein Binding
  • Repressor Proteins / chemistry
  • Repressor Proteins / metabolism
  • Repressor Proteins / physiology*
  • Sin3 Histone Deacetylase and Corepressor Complex
  • Structure-Activity Relationship
  • Surface Plasmon Resonance


  • DNA Primers
  • Nucleic Acids
  • Repressor Proteins
  • SIN3A transcription factor
  • Sap30 protein, mouse
  • Histone Deacetylases
  • Sin3 Histone Deacetylase and Corepressor Complex

Associated data

  • PDB/2LD7