1. Structural Biology and Molecular Biophysics

Structure-based nuclear import mechanism of histones H3 and H4 mediated by Kap123

  1. Sojin An
  2. Jungmin Yoon
  3. Hanseong Kim
  4. Ji-Joon Song
  5. Uhn-soo Cho  Is a corresponding author
  1. University of Michigan Medical School, United States
  2. Korea Advanced Institute of Science and Technology, Korea (South), Republic of
https://doi.org/10.7554/eLife.30244
Share this article
Cite this article
  1. Sojin An
  2. Jungmin Yoon
  3. Hanseong Kim
  4. Ji-Joon Song
  5. Uhn-soo Cho
(2017)
Structure-based nuclear import mechanism of histones H3 and H4 mediated by Kap123
eLife 6:e30244.
https://doi.org/10.7554/eLife.30244
  2. Download BibTeX
  3. Download .RIS

Abstract

Kap123, a major karyopherin protein of budding yeast, recognizes the nuclear localization signals (NLSs) of cytoplasmic histones H3 and H4 and translocates them into the nucleus during DNA replication. Mechanistic questions include H3- and H4-NLS redundancy toward Kap123 and the role of the conserved diacetylation of cytoplasmic H4 (K5ac and K12ac) in Kap123-mediated histone nuclear translocation. Here, we report crystal structures of full-length Kluyveromyces lactis Kap123 alone and in complex with H3- and H4-NLSs. Structures reveal the unique feature of Kap123 that possesses two discrete lysine-binding pockets for NLS recognition. Structural comparison illustrates that H3- and H4-NLSs share at least one of two lysine-binding pockets, suggesting that H3- and H4-NLSs are mutually exclusive. Additionally, acetylation of key lysine residues at NLS, particularly H4-NLS diacetylation, weakens the interaction with Kap123. These data support that cytoplasmic histone H4 diacetylation weakens the Kap123-H4-NLS interaction thereby facilitating histone Kap123-H3-dependent H3:H4/Asf1 complex nuclear translocation.

Data availability

The following data sets were generated

Article and author information

Author details

  1. Sojin An

    Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Jungmin Yoon

    Structural Biology Laboratory of Epigenetics, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea (South), Republic of
    Competing interests
    The authors declare that no competing interests exist.

  3. Hanseong Kim

    Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Ji-Joon Song

    Structural Biology Laboratory of Epigenetics, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea (South), Republic of
    Competing interests
    The authors declare that no competing interests exist.

  5. Uhn-soo Cho

    Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, United States
    For correspondence
    uhnsoo@med.umich.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6992-2455

Funding

National Institutes of Health (DK111465)

  • Uhn-soo Cho

American Diabetes Association (1-16-JDF-017)

  • Uhn-soo Cho

National Institutes of Health (AG050903)

  • Uhn-soo Cho

March of Dimes Foundation (N019154-00)

  • Uhn-soo Cho

National Research Foundation of Korea (2016R1A2B3006293)

  • Ji-Joon Song

National Research Foundation of Korea (2013R1A1A2055605)

  • Ji-Joon Song

National Research Foundation of Korea (2014K2A3A1000137)

  • Ji-Joon Song

National Research Foundation of Korea (2011-0031955)

  • Ji-Joon Song

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Eric Campos, The Hospital for Sick Children, Canada

Version history

  1. Received: July 7, 2017
  2. Accepted: October 12, 2017
  3. Accepted Manuscript published: October 16, 2017 (version 1)
  4. Version of Record published: November 8, 2017 (version 2)

Copyright

© 2017, An et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,466
    views
  • 384
    downloads
  • 18
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Sojin An
  2. Jungmin Yoon
  3. Hanseong Kim
  4. Ji-Joon Song
  5. Uhn-soo Cho
(2017)
Structure-based nuclear import mechanism of histones H3 and H4 mediated by Kap123
eLife 6:e30244.
https://doi.org/10.7554/eLife.30244

Share this article

https://doi.org/10.7554/eLife.30244

Categories and tags

Further reading

    1. Structural Biology and Molecular Biophysics

    The mechanism of mammalian proton-coupled peptide transporters

    Simon M Lichtinger, Joanne L Parker ... Philip C Biggin
    Research Article

    Proton-coupled oligopeptide transporters (POTs) are of great pharmaceutical interest owing to their promiscuous substrate binding site that has been linked to improved oral bioavailability of several classes of drugs. Members of the POT family are conserved across all phylogenetic kingdoms and function by coupling peptide uptake to the proton electrochemical gradient. Cryo-EM structures and alphafold models have recently provided new insights into different conformational states of two mammalian POTs, SLC15A1, and SLC15A2. Nevertheless, these studies leave open important questions regarding the mechanism of proton and substrate coupling, while simultaneously providing a unique opportunity to investigate these processes using molecular dynamics (MD) simulations. Here, we employ extensive unbiased and enhanced-sampling MD to map out the full SLC15A2 conformational cycle and its thermodynamic driving forces. By computing conformational free energy landscapes in different protonation states and in the absence or presence of peptide substrate, we identify a likely sequence of intermediate protonation steps that drive inward-directed alternating access. These simulations identify key differences in the extracellular gate between mammalian and bacterial POTs, which we validate experimentally in cell-based transport assays. Our results from constant-PH MD and absolute binding free energy (ABFE) calculations also establish a mechanistic link between proton binding and peptide recognition, revealing key details underpining secondary active transport in POTs. This study provides a vital step forward in understanding proton-coupled peptide and drug transport in mammals and pave the way to integrate knowledge of solute carrier structural biology with enhanced drug design to target tissue and organ bioavailability.

    1. Structural Biology and Molecular Biophysics

    Plasticity of the proteasome-targeting signal Fat10 enhances substrate degradation

    Hitendra Negi, Aravind Ravichandran ... Ranabir Das
    Research Article

    The proteasome controls levels of most cellular proteins, and its activity is regulated under stress, quiescence, and inflammation. However, factors determining the proteasomal degradation rate remain poorly understood. Proteasome substrates are conjugated with small proteins (tags) like ubiquitin and Fat10 to target them to the proteasome. It is unclear if the structural plasticity of proteasome-targeting tags can influence substrate degradation. Fat10 is upregulated during inflammation, and its substrates undergo rapid proteasomal degradation. We report that the degradation rate of Fat10 substrates critically depends on the structural plasticity of Fat10. While the ubiquitin tag is recycled at the proteasome, Fat10 is degraded with the substrate. Our results suggest significantly lower thermodynamic stability and faster mechanical unfolding in Fat10 compared to ubiquitin. Long-range salt bridges are absent in the Fat10 structure, creating a plastic protein with partially unstructured regions suitable for proteasome engagement. Fat10 plasticity destabilizes substrates significantly and creates partially unstructured regions in the substrate to enhance degradation. NMR-relaxation-derived order parameters and temperature dependence of chemical shifts identify the Fat10-induced partially unstructured regions in the substrate, which correlated excellently to Fat10-substrate contacts, suggesting that the tag-substrate collision destabilizes the substrate. These results highlight a strong dependence of proteasomal degradation on the structural plasticity and thermodynamic properties of the proteasome-targeting tags.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Special Issue: Allosteric regulation of kinase activity

    Amy H Andreotti, Volker Dötsch
    Editorial

    The articles in this special issue highlight how modern cellular, biochemical, biophysical and computational techniques are allowing deeper and more detailed studies of allosteric kinase regulation.