Structural and biochemical analyses of the DEAD-box ATPase Sub2 in association with THO or Yra1

Elife. 2017 Jan 6;6:e20070. doi: 10.7554/eLife.20070.

Abstract

mRNA is cotranscrptionally processed and packaged into messenger ribonucleoprotein particles (mRNPs) in the nucleus. Prior to export through the nuclear pore, mRNPs undergo several obligatory remodeling reactions. In yeast, one of these reactions involves loading of the mRNA-binding protein Yra1 by the DEAD-box ATPase Sub2 as assisted by the hetero-pentameric THO complex. To obtain molecular insights into reaction mechanisms, we determined crystal structures of two relevant complexes: a THO hetero-pentamer bound to Sub2 at 6.0 Å resolution; and Sub2 associated with an ATP analogue, RNA, and a C-terminal fragment of Yra1 (Yra1-C) at 2.6 Å resolution. We found that the 25 nm long THO clamps Sub2 in a half-open configuration; in contrast, when bound to the ATP analogue, RNA and Yra1-C, Sub2 assumes a closed conformation. Both THO and Yra1-C stimulated Sub2's intrinsic ATPase activity. We propose that THO surveys common landmarks in each nuclear mRNP to localize Sub2 for targeted loading of Yra1.

Keywords: DEAD-box ATPase; S. cerevisiae; X-ray crystallography; biochemistry; biophysics; mRNP remodeling; structural biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases / chemistry*
  • Adenosine Triphosphatases / metabolism*
  • Crystallography, X-Ray
  • Models, Molecular
  • Nuclear Proteins / chemistry*
  • Nuclear Proteins / metabolism*
  • Protein Conformation
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / metabolism*
  • Ribonucleoproteins / chemistry
  • Ribonucleoproteins / metabolism
  • Saccharomyces cerevisiae / enzymology*
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Transcription Factors / chemistry*
  • Transcription Factors / metabolism*

Substances

  • Nuclear Proteins
  • RNA-Binding Proteins
  • Ribonucleoproteins
  • Saccharomyces cerevisiae Proteins
  • THO2 protein, S cerevisiae
  • Transcription Factors
  • YRA1 protein, S cerevisiae
  • messenger ribonucleoprotein
  • Adenosine Triphosphatases
  • RNA-dependent ATPase