MutS/MutL crystal structure reveals that the MutS sliding clamp loads MutL onto DNA

  1. Flora S Groothuizen
  2. Ines Winkler
  3. Michele Cristóvão
  4. Alexander Fish
  5. Herrie H K Winterwerp
  6. Annet Reumer
  7. Andreas D Marx
  8. Nicolaas Hermans
  9. Robert A Nicholls
  10. Garib N Murshudov
  11. Joyce H G Lebbink
  12. Peter Friedhoff
  13. Titia K Sixma  Is a corresponding author
  1. Netherlands Cancer Institute, Netherlands
  2. Justus-Liebig-University, Germany
  3. Erasmus Medical Center, Netherlands
  4. MRC Laboratory of Molecular Biology, United Kingdom

Abstract

To avoid mutations in the genome, DNA replication is generally followed by DNA mismatch repair (MMR). MMR starts when a MutS homolog recognizes a mismatch and undergoes an ATP-dependent transformation to an elusive sliding clamp state. How this transient state promotes MutL homolog recruitment and activation of repair is unclear. Here we present a crystal structure of the MutS/MutL complex using a site-specifically crosslinked complex and examine how large conformational changes lead to activation of MutL. The structure captures MutS in the sliding clamp conformation, where tilting of the MutS subunits across each other pushes DNA into a new channel, and reorientation of the connector domain creates an interface for MutL with both MutS subunits. Our work explains how the sliding clamp promotes loading of MutL onto DNA, to activate downstream effectors. We thus elucidate a crucial mechanism that ensures that MMR is initiated only after detection of a DNA mismatch.

Article and author information

Author details

  1. Flora S Groothuizen

    Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Amsterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  2. Ines Winkler

    Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Michele Cristóvão

    Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Alexander Fish

    Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Amsterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  5. Herrie H K Winterwerp

    Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Amsterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  6. Annet Reumer

    Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Amsterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  7. Andreas D Marx

    Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  8. Nicolaas Hermans

    Department of Genetics, Cancer Genomics Netherlands, Erasmus Medical Center, Rotterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  9. Robert A Nicholls

    Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  10. Garib N Murshudov

    Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  11. Joyce H G Lebbink

    Department of Genetics, Cancer Genomics Netherlands, Erasmus Medical Center, Rotterdam, Netherlands
    Competing interests
    The authors declare that no competing interests exist.
  12. Peter Friedhoff

    Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  13. Titia K Sixma

    Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Amsterdam, Netherlands
    For correspondence
    t.sixma@nki.nl
    Competing interests
    The authors declare that no competing interests exist.

Copyright

© 2015, Groothuizen 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

  • 5,806
    views
  • 1,176
    downloads
  • 92
    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. Flora S Groothuizen
  2. Ines Winkler
  3. Michele Cristóvão
  4. Alexander Fish
  5. Herrie H K Winterwerp
  6. Annet Reumer
  7. Andreas D Marx
  8. Nicolaas Hermans
  9. Robert A Nicholls
  10. Garib N Murshudov
  11. Joyce H G Lebbink
  12. Peter Friedhoff
  13. Titia K Sixma
(2015)
MutS/MutL crystal structure reveals that the MutS sliding clamp loads MutL onto DNA
eLife 4:e06744.
https://doi.org/10.7554/eLife.06744

Share this article

https://doi.org/10.7554/eLife.06744

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Cristina Paissoni, Sarita Puri ... Carlo Camilloni
    Research Article

    Both immunoglobulin light-chain (LC) amyloidosis (AL) and multiple myeloma (MM) share the overproduction of a clonal LC. However, while LCs in MM remain soluble in circulation, AL LCs misfold into toxic-soluble species and amyloid fibrils that accumulate in organs, leading to distinct clinical manifestations. The significant sequence variability of LCs has hindered the understanding of the mechanisms driving LC aggregation. Nevertheless, emerging biochemical properties, including dimer stability, conformational dynamics, and proteolysis susceptibility, distinguish AL LCs from those in MM under native conditions. This study aimed to identify a2 conformational fingerprint distinguishing AL from MM LCs. Using small-angle X-ray scattering (SAXS) under native conditions, we analyzed four AL and two MM LCs. We observed that AL LCs exhibited a slightly larger radius of gyration and greater deviations from X-ray crystallography-determined or predicted structures, reflecting enhanced conformational dynamics. SAXS data, integrated with molecular dynamics simulations, revealed a conformational ensemble where LCs adopt multiple states, with variable and constant domains either bent or straight. AL LCs displayed a distinct, low-populated, straight conformation (termed H state), which maximized solvent accessibility at the interface between constant and variable domains. Hydrogen-deuterium exchange mass spectrometry experimentally validated this H state. These findings reconcile diverse experimental observations and provide a precise structural target for future drug design efforts.

    1. Structural Biology and Molecular Biophysics
    Kingsley Y Wu, Ta I Hung, Chia-en A Chang
    Research Article

    PROteolysis TArgeting Chimeras (PROTACs) are small molecules that induce target protein degradation via the ubiquitin-proteasome system. PROTACs recruit the target protein and E3 ligase; a critical first step is forming a ternary complex. However, while the formation of a ternary complex is crucial, it may not always guarantee successful protein degradation. The dynamics of the PROTAC-induced degradation complex play a key role in ubiquitination and subsequent degradation. In this study, we computationally modelled protein complex structures and dynamics associated with a series of PROTACs featuring different linkers to investigate why these PROTACs, all of which formed ternary complexes with Cereblon (CRBN) E3 ligase and the target protein bromodomain-containing protein 4 (BRD4BD1), exhibited varying degrees of degradation potency. We constructed the degradation machinery complexes with Culling-Ring Ligase 4A (CRL4A) E3 ligase scaffolds. Through atomistic molecular dynamics simulations, we illustrated how PROTAC-dependent protein dynamics facilitating the arrangement of surface lysine residues of BRD4BD1 into the catalytic pocket of E2/ubiquitin cascade for ubiquitination. Despite featuring identical warheads in this PROTAC series, the linkers were found to affect the residue-interaction networks, and thus governing the essential motions of the entire degradation machine for ubiquitination. These findings offer a structural dynamic perspective on ligand-induced protein degradation, providing insights to guide future PROTAC design endeavors.