Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity

  1. Zhijie Lin
  2. Zhou Yang
  3. Ruiling Xie
  4. Zeyang Ji
  5. Kunliang Guan
  6. Mingjie Zhang  Is a corresponding author
  1. Hong Kong University of Science and Technology, Hong Kong
  2. University of California, San Diego, United States

Abstract

WW domain tandem-containing proteins such as KIBRA, YAP, and MAGI play critical roles in cell growth and polarity via binding to and positioning target proteins in specific subcellular regions. An immense disparity exists between promiscuity of WW domain-mediated target bindings and specific roles of WW domain proteins in cell growth regulation. Here, we discovered that WW domain tandems of KIBRA and MAGI, but not YAP, bind to specific target proteins with extremely high affinity and exquisite sequence specificity. Via systematic structural biology and biochemistry approaches, we decoded the target binding rules of WW domain tandems from cell growth regulatory proteins and uncovered a list of previously unknown WW tandem binding proteins including β-Dystroglycan, JCAD, and PTPN21. The WW tandem-mediated target recognition mechanisms elucidated here can guide functional studies of WW domain proteins in cell growth and polarity as well as in other cellular processes including neuronal synaptic signaling.

Data availability

The atomic coordinates of the WW tandem and target complex structures have been deposited to the Protein Data Bank under the accession codes of: 6J68 (KIBRA/LATS1), 6JJW (KIBRA/PTPN14), 6JJX (KBIRA/AMOT), 6JJY (KIBRA/β-DG), 6JJZ (MAGI2/Dendrin), 6JK0 (YAP-Linker-Dendrin), and 6JK1 (Dendrin-Linker-YAP).

The following data sets were generated

Article and author information

Author details

  1. Zhijie Lin

    Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, Hong Kong
    Competing interests
    No competing interests declared.
  2. Zhou Yang

    Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, Hong Kong
    Competing interests
    No competing interests declared.
  3. Ruiling Xie

    Department of Pharmacology, University of California, San Diego, La Jolla, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6086-8683
  4. Zeyang Ji

    Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, Hong Kong
    Competing interests
    No competing interests declared.
  5. Kunliang Guan

    Department of Pharmacology, University of California, San Diego, La Jolla, United States
    Competing interests
    Kunliang Guan, co-founder and has an equity interest in Vivace Therapeutics, Inc. The terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies.
  6. Mingjie Zhang

    Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, Hong Kong
    For correspondence
    mzhang@ust.hk
    Competing interests
    Mingjie Zhang, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9404-0190

Funding

Asia Foundation for Cancer Research (AFCR17SC01)

  • Mingjie Zhang

National Institutes of Health (CA196878)

  • Kunliang Guan

Research Grants Council, University Grants Committee (AOE-M09-12)

  • Mingjie Zhang

Research Grants Council, University Grants Committee (C6004-17G)

  • Mingjie Zhang

National Institutes of Health (CA217642)

  • Kunliang Guan

National Institutes of Health (GM51586)

  • Kunliang Guan

National Institutes of Health (DEO15964)

  • Kunliang Guan

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

Copyright

© 2019, Lin 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

  • 3,168
    views
  • 501
    downloads
  • 42
    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. Zhijie Lin
  2. Zhou Yang
  3. Ruiling Xie
  4. Zeyang Ji
  5. Kunliang Guan
  6. Mingjie Zhang
(2019)
Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity
eLife 8:e49439.
https://doi.org/10.7554/eLife.49439

Share this article

https://doi.org/10.7554/eLife.49439

Further reading

    1. Structural Biology and Molecular Biophysics
    Giuseppe Deganutti, Ludovico Pipito ... Christopher Arthur Reynolds
    Research Article

    The structural basis for the pharmacology of human G protein-coupled receptors (GPCRs), the most abundant membrane proteins and the target of about 35% of approved drugs, is still a matter of intense study. What makes GPCRs challenging to study is the inherent flexibility and the metastable nature of interaction with extra- and intracellular partners that drive their effects. Here, we present a molecular dynamics (MD) adaptive sampling algorithm, namely multiple walker supervised molecular dynamics (mwSuMD), to address complex structural transitions involving GPCRs without energy input. We first report the binding and unbinding of the vasopressin peptide from its receptor V2. Successively, we present the complete transition of the glucagon-like peptide-1 receptor (GLP-1R) from inactive to active, agonist and Gs-bound state, and the guanosine diphosphate (GDP) release from Gs. To our knowledge, this is the first time the whole sequence of events leading from an inactive GPCR to the GDP release is simulated without any energy bias. We demonstrate that mwSuMD can address complex binding processes intrinsically linked to protein dynamics out of reach of classic MD.

    1. Structural Biology and Molecular Biophysics
    Jesse Howe, Douglas Walker ... Elisar J Barbar
    Research Article

    53BP1 is a key player in DNA repair and together with BRCA1 regulate selection of DNA double strand break repair mechanisms. Localization of DNA repair factors to sites of DNA damage by 53BP1 is controlled by its oligomerization domain (OD) and binding to LC8, a hub protein that functions to dimerize >100 clients. Here we show that 53BP1 OD is a trimer, an unusual finding for LC8 clients which are all dimers or tetramers. As a trimer, 53BP1 forms a heterogeneous mixture of complexes when bound to dimeric LC8 with the largest mass corresponding to a dimer-of-trimers bridged by 3 LC8 dimers. Analytical ultracentrifugation and isothermal titration calorimetry demonstrate that only the second of the three LC8 recognition motifs is necessary for a stable bridged complex. The stability of the bridged complex is tuned by multivalency, binding specificity of the second LC8 site, and the length of the linker separating the LC8 binding domain and OD. 53BP1 mutants deficient in bridged species fail to impact 53BP1 focus formation in human cell culture studies, suggesting that the primary role of LC8 is to bridge 53BP1 trimers which in turn promotes recruitment of 53BP1 at sites of DNA damage. We propose that the formation of higher-order oligomers of 53BP1 explains how LC8 elicits an improvement in 53BP1 foci and affects the structure and functions of 53BP1.