Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1 at 3.7 angstrom resolution

Elife. 2017 Aug 2;6:e28384. doi: 10.7554/eLife.28384.

Abstract

Coactivator complexes SAGA and NuA4 stimulate transcription by post-translationally modifying chromatin. Both complexes contain the Tra1 subunit, a highly conserved 3744-residue protein from the Phosphoinositide 3-Kinase-related kinase (PIKK) family and a direct target for multiple sequence-specific activators. We present the Cryo-EM structure of Saccharomyces cerevsisae Tra1 to 3.7 Å resolution, revealing an extensive network of alpha-helical solenoids organized into a diamond ring conformation and is strikingly reminiscent of DNA-PKcs, suggesting a direct role for Tra1 in DNA repair. The structure was fitted into an existing SAGA EM reconstruction and reveals limited contact surfaces to Tra1, hence it does not act as a molecular scaffold within SAGA. Mutations that affect activator targeting are distributed across the Tra1 structure, but also cluster within the N-terminal Finger region, indicating the presence of an activator interaction site. The structure of Tra1 is a key milestone in deciphering the mechanism of multiple coactivator complexes.

Keywords: NuA4; PIKK; S. cerevisiae; SAGA; biophysics; chromatin; chromosomes; coactivator; genes; structural biology; transcription activation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Binding Sites
  • Chromatin / chemistry*
  • Chromatin / metabolism
  • Cloning, Molecular
  • Cryoelectron Microscopy
  • DNA Repair
  • DNA, Fungal / chemistry*
  • DNA, Fungal / genetics
  • DNA, Fungal / metabolism
  • Gene Expression
  • Histone Acetyltransferases / chemistry*
  • Histone Acetyltransferases / genetics
  • Histone Acetyltransferases / metabolism
  • Plasmids / chemistry
  • Plasmids / metabolism
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Interaction Domains and Motifs
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Saccharomyces cerevisiae / enzymology
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • Trans-Activators / chemistry*
  • Trans-Activators / genetics
  • Trans-Activators / metabolism

Substances

  • Chromatin
  • DNA, Fungal
  • Recombinant Proteins
  • SAGA complex, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • TRA1 protein, S cerevisiae
  • Trans-Activators
  • Histone Acetyltransferases
  • NuA4 protein, S cerevisiae