The pentameric nucleoplasmin fold is present in Drosophila FKBP39 and a large number of chromatin-related proteins

J Mol Biol. 2015 May 22;427(10):1949-63. doi: 10.1016/j.jmb.2015.03.010. Epub 2015 Mar 24.

Abstract

Nucleoplasmin is a histone chaperone that consists of a pentameric N-terminal domain and an unstructured C-terminal tail. The pentameric core domain, a doughnut-like structure with a central pore, is only found in the nucleoplasmin family. Here, we report the first structure of a nucleoplasmin-like domain (NPL) from the unrelated Drosophila protein, FKBP39, and we present evidence that this protein associates with chromatin. Furthermore, we show that two other chromatin proteins, Arabidopsis thaliana histone deacetylase type 2 (HD2) and Saccharomyces cerevisiae Fpr4, share the NPL fold and form pentamers, or a dimer of pentamers in the case of HD2. Thus, we propose a new family of proteins that share the pentameric nucleoplasmin-like NPL domain and are found in protists, fungi, plants and animals.

Keywords: FKBP; NMR; histone chaperone; nucleoplasmin; structure determination.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Arabidopsis / metabolism
  • Chromatin / metabolism*
  • Cross-Linking Reagents
  • Crystallography, X-Ray
  • Drosophila Proteins / chemistry*
  • Drosophila Proteins / metabolism
  • Drosophila melanogaster / metabolism
  • Histone Chaperones / chemistry*
  • Histone Chaperones / metabolism
  • Histone Deacetylase 2 / chemistry*
  • Histone Deacetylase 2 / metabolism
  • Histones / metabolism*
  • Immunoprecipitation
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleoplasmins / chemistry*
  • Nucleoplasmins / metabolism
  • Phylogeny
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Tertiary
  • Recombinant Proteins / chemistry*
  • Recombinant Proteins / metabolism
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / metabolism
  • Sequence Homology, Amino Acid
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
  • Structure-Activity Relationship
  • Tacrolimus Binding Proteins / chemistry*
  • Tacrolimus Binding Proteins / metabolism

Substances

  • Chromatin
  • Cross-Linking Reagents
  • Drosophila Proteins
  • FKBP39 protein, Drosophila
  • Histone Chaperones
  • Histones
  • Nucleoplasmins
  • Recombinant Proteins
  • Saccharomyces cerevisiae Proteins
  • Histone Deacetylase 2
  • Tacrolimus Binding Proteins
  • Fpr4 protein, S cerevisiae