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Structure of the MutLα C-terminal domain reveals how Mlh1 contributes to Pms1 endonuclease site

Nature Structural & Molecular Biology volume 20, pages 461–468 (2013)Cite this article

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Abstract

Mismatch-repair factors have a prominent role in surveying eukaryotic DNA-replication fidelity and in ensuring correct meiotic recombination. These functions depend on MutL-homolog heterodimers with Mlh1. In humans, MLH1 mutations underlie half of hereditary nonpolyposis colorectal cancers (HNPCCs). Here we report crystal structures of the MutLα (Mlh1–Pms1 heterodimer) C-terminal domain (CTD) from Saccharomyces cerevisiae, alone and in complex with fragments derived from Mlh1 partners. These structures reveal structural rearrangements and additional domains in MutLα as compared to the bacterial MutL counterparts and show that the strictly conserved C terminus of Mlh1 forms part of the Pms1 endonuclease site. The structures of the ternary complexes between MutLα(CTD) and Exo1 or Ntg2 fragments reveal the binding mode of the MIP-box motif shared by several Mlh1 partners. Finally, the structures provide a rationale for the deleterious impact of MLH1 mutations in HNPCCs.

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Figure 1: Crystal structure of MutLα(CTD).
Figure 2: MutLα heterodimerization patches.
Figure 3: MutLα endonuclease site.
Figure 4: Structures of ternary complexes between MutLα(CTD) and MIP box–containing fragments.
Figure 5: Mapping of deleterious mutations associated with HNPCC cancers.

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References

  1. Iyer, R.R., Pluciennik, A., Burdett, V. & Modrich, P.L. DNA mismatch repair: functions and mechanisms. Chem. Rev. 106, 302–323 (2006).

    Article  CAS  Google Scholar 

  2. Kunkel, T.A. & Erie, D.A. DNA mismatch repair. Annu. Rev. Biochem. 74, 681–710 (2005).

    Article  CAS  Google Scholar 

  3. Jiricny, J. The multifaceted mismatch-repair system. Nat. Rev. Mol. Cell Biol. 7, 335–346 (2006).

    Article  CAS  Google Scholar 

  4. Lagerstedt Robinson, K. et al. Lynch syndrome (hereditary nonpolyposis colorectal cancer) diagnostics. J. Natl. Cancer Inst. 99, 291–299 (2007).

    Article  Google Scholar 

  5. Lynch, H.T. et al. Review of the Lynch syndrome: history, molecular genetics, screening, differential diagnosis, and medicolegal ramifications. Clin. Genet. 76, 1–18 (2009).

    Article  CAS  Google Scholar 

  6. Gorman, J. et al. Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6. Mol. Cell 28, 359–370 (2007).

    Article  CAS  Google Scholar 

  7. Jeong, C. et al. MutS switches between two fundamentally distinct clamps during mismatch repair. Nat. Struct. Mol. Biol. 18, 379–385 (2011).

    Article  CAS  Google Scholar 

  8. Warren, J.J. et al. Structure of the human MutSα DNA lesion recognition complex. Mol. Cell 26, 579–592 (2007).

    Article  CAS  Google Scholar 

  9. Acharya, S., Foster, P.L., Brooks, P. & Fishel, R. The coordinated functions of the E. coli MutS and MutL proteins in mismatch repair. Mol. Cell 12, 233–246 (2003).

    Article  CAS  Google Scholar 

  10. Kadyrov, F.A., Dzantiev, L., Constantin, N. & Modrich, P. Endonucleolytic function of MutLα in human mismatch repair. Cell 126, 297–308 (2006).

    Article  CAS  Google Scholar 

  11. Kadyrov, F.A. et al. Saccharomyces cerevisiae MutLα is a mismatch repair endonuclease. J. Biol. Chem. 282, 37181–37190 (2007).

    Article  CAS  Google Scholar 

  12. Kosinski, J., Plotz, G., Guarne, A., Bujnicki, J.M. & Friedhoff, P. The PMS2 subunit of human MutLα contains a metal ion binding domain of the iron-dependent repressor protein family. J. Mol. Biol. 382, 610–627 (2008).

    Article  CAS  Google Scholar 

  13. van Oers, J.M. et al. PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance. Proc. Natl. Acad. Sci. USA 107, 13384–13389 (2010).

    Article  CAS  Google Scholar 

  14. Ban, C., Junop, M. & Yang, W. Transformation of MutL by ATP binding and hydrolysis: a switch in DNA mismatch repair. Cell 97, 85–97 (1999).

    Article  CAS  Google Scholar 

  15. Wang, T.F., Kleckner, N. & Hunter, N. Functional specificity of MutL homologs in yeast: evidence for three Mlh1-based heterocomplexes with distinct roles during meiosis in recombination and mismatch correction. Proc. Natl. Acad. Sci. USA 96, 13914–13919 (1999).

    Article  CAS  Google Scholar 

  16. Gorman, J., Plys, A.J., Visnapuu, M.L., Alani, E. & Greene, E.C. Visualizing one-dimensional diffusion of eukaryotic DNA repair factors along a chromatin lattice. Nat. Struct. Mol. Biol. 17, 932–938 (2010).

    Article  CAS  Google Scholar 

  17. Sacho, E.J., Kadyrov, F.A., Modrich, P., Kunkel, T.A. & Erie, D.A. Direct visualization of asymmetric adenine nucleotide-induced conformational changes in MutLα. Mol. Cell 29, 112–121 (2008).

    Article  CAS  Google Scholar 

  18. Arana, M.E. et al. Functional residues on the surface of the N-terminal domain of yeast Pms1. DNA Repair (Amst.) 9, 448–457 (2010).

    Article  CAS  Google Scholar 

  19. Guarné, A., Junop, M.S. & Yang, W. Structure and function of the N-terminal 40 kDa fragment of human PMS2: a monomeric GHL ATPase. EMBO J. 20, 5521–5531 (2001).

    Article  Google Scholar 

  20. Tran, P.T. & Liskay, R.M. Functional studies on the candidate ATPase domains of Saccharomyces cerevisiae MutLα. Mol. Cell Biol. 20, 6390–6398 (2000).

    Article  CAS  Google Scholar 

  21. Pang, Q., Prolla, T.A. & Liskay, R.M. Functional domains of the Saccharomyces cerevisiae Mlh1p and Pms1p DNA mismatch repair proteins and their relevance to human hereditary nonpolyposis colorectal cancer-associated mutations. Mol. Cell Biol. 17, 4465–4473 (1997).

    Article  CAS  Google Scholar 

  22. Deschênes, S.M. et al. The E705K mutation in hPMS2 exerts recessive, not dominant, effects on mismatch repair. Cancer Lett. 249, 148–156 (2007).

    Article  Google Scholar 

  23. Erdeniz, N., Nguyen, M., Deschenes, S.M. & Liskay, R.M. Mutations affecting a putative MutLα endonuclease motif impact multiple mismatch repair functions. DNA Repair (Amst.) 6, 1463–1470 (2007).

    Article  CAS  Google Scholar 

  24. Guarné, A. et al. Structure of the MutL C-terminal domain: a model of intact MutL and its roles in mismatch repair. EMBO J. 23, 4134–4145 (2004).

    Article  Google Scholar 

  25. Namadurai, S. et al. The C-terminal domain of the MutL homolog from Neisseria gonorrhoeae forms an inverted homodimer. PLoS ONE 5, e13726 (2010).

    Article  Google Scholar 

  26. Pillon, M.C. et al. Structure of the endonuclease domain of MutL: unlicensed to cut. Mol. Cell 39, 145–151 (2010).

    Article  CAS  Google Scholar 

  27. Kosinski, J., Steindorf, I., Bujnicki, J.M., Giron-Monzon, L. & Friedhoff, P. Analysis of the quaternary structure of the MutL C-terminal domain. J. Mol. Biol. 351, 895–909 (2005).

    Article  CAS  Google Scholar 

  28. Fukui, K. DNA mismatch repair in eukaryotes and bacteria. J. Nucleic Acids 2010, 1–16 (2010).

    Article  Google Scholar 

  29. Chao, E.C. et al. Accurate classification of MLH1/MSH2 missense variants with multivariate analysis of protein polymorphisms-mismatch repair (MAPP-MMR). Hum. Mutat. 29, 852–860 (2008).

    Article  CAS  Google Scholar 

  30. Kosinski, J., Hinrichsen, I., Bujnicki, J.M., Friedhoff, P. & Plotz, G. Identification of Lynch syndrome mutations in the MLH1–PMS2 interface that disturb dimerization and mismatch repair. Hum. Mutat. 31, 975–982 (2010).

    Article  CAS  Google Scholar 

  31. Takahashi, M. et al. Functional analysis of human MLH1 variants using yeast and in vitro mismatch repair assays. Cancer Res. 67, 4595–4604 (2007).

    Article  CAS  Google Scholar 

  32. Cutalo, J.M., Darden, T.A., Kunkel, T.A. & Tomer, K.B. Mapping the dimer interface in the C-terminal domains of the yeast MLH1–PMS1 heterodimer. Biochemistry 45, 15458–15467 (2006).

    Article  CAS  Google Scholar 

  33. Gellon, L., Werner, M. & Boiteux, S. Ntg2p, a Saccharomyces cerevisiae DNA N-glycosylase/apurinic or apyrimidinic lyase involved in base excision repair of oxidative DNA damage, interacts with the DNA mismatch repair protein Mlh1p. Identification of a Mlh1p binding motif. J. Biol. Chem. 277, 29963–29972 (2002).

    Article  CAS  Google Scholar 

  34. Pedrazzi, G. et al. Direct association of Bloom's syndrome gene product with the human mismatch repair protein MLH1. Nucleic Acids Res. 29, 4378–4386 (2001).

    Article  CAS  Google Scholar 

  35. Tran, P.T., Simon, J.A. & Liskay, R.M. Interactions of Exo1p with components of MutLα in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 98, 9760–9765 (2001).

    Article  CAS  Google Scholar 

  36. Dherin, C. et al. Characterization of a highly conserved binding site of Mlh1 required for exonuclease I-dependent mismatch repair. Mol. Cell Biol. 29, 907–918 (2009).

    Article  CAS  Google Scholar 

  37. Zakharyevich, K. et al. Temporally and biochemically distinct activities of Exo1 during meiosis: double-strand break resection and resolution of double Holliday junctions. Mol. Cell 40, 1001–1015 (2010).

    Article  CAS  Google Scholar 

  38. Mauris, J. & Evans, T.C. Adenosine triphosphate stimulates Aquifex aeolicus MutL endonuclease activity. PLoS ONE 4, e7175 (2009).

    Article  Google Scholar 

  39. Aurora, R., Creamer, T.P., Srinivasan, R. & Rose, G.D. Local interactions in protein folding: lessons from the α-helix. J. Biol. Chem. 272, 1413–1416 (1997).

    Article  CAS  Google Scholar 

  40. Duddy, W.J., Nissink, J.W., Allen, F.H. & Milner-White, E.J. Mimicry by asx- and ST-turns of the four main types of β-turn in proteins. Protein Sci. 13, 3051–3055 (2004).

    Article  CAS  Google Scholar 

  41. Fiser, A. & Sali, A. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol. 374, 461–491 (2003).

    Article  CAS  Google Scholar 

  42. Umar, A. et al. Requirement for PCNA in DNA mismatch repair at a step preceding DNA resynthesis. Cell 87, 65–73 (1996).

    Article  CAS  Google Scholar 

  43. Bellacosa, A. et al. MED1, a novel human methyl-CpG-binding endonuclease, interacts with DNA mismatch repair protein MLH1. Proc. Natl. Acad. Sci. USA 96, 3969–3974 (1999).

    Article  CAS  Google Scholar 

  44. Cannavo, E., Gerrits, B., Marra, G., Schlapbach, R. & Jiricny, J. Characterization of the interactome of the human MutL homologues MLH1, PMS1, and PMS2. J. Biol. Chem. 282, 2976–2986 (2007).

    Article  CAS  Google Scholar 

  45. Amin, N.S., Nguyen, M.N., Oh, S. & Kolodner, R.D. exo1-Dependent mutator mutations: model system for studying functional interactions in mismatch repair. Mol. Cell Biol. 21, 5142–5155 (2001).

    Article  CAS  Google Scholar 

  46. Tran, P.T. et al. A mutation in EXO1 defines separable roles in DNA mismatch repair and post-replication repair. DNA Repair (Amst.) 6, 1572–1583 (2007).

    Article  CAS  Google Scholar 

  47. Lee, S.D. & Alani, E. Analysis of interactions between mismatch repair initiation factors and the replication processivity factor PCNA. J. Mol. Biol. 355, 175–184 (2006).

    Article  CAS  Google Scholar 

  48. Jo, S., Vargyas, M., Vasko-Szedlar, J., Roux, B. & Im, W. PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Res. 36, W270–W275 (2008).

    Article  CAS  Google Scholar 

  49. Inoue, H., Nojima, H. & Okayama, H. High efficiency transformation of Escherichia coli with plasmids. Gene 96, 23–28 (1990).

    Article  CAS  Google Scholar 

  50. Kabsch, W. Xds. Acta Crystallogr. D Biol. Crystallogr. 66, 125–132 (2010).

    Article  CAS  Google Scholar 

  51. Sheldrick, G.M. A short history of SHELX. Acta Crystallogr. A 64, 112–122 (2008).

    Article  CAS  Google Scholar 

  52. McCoy, A.J. Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr. D Biol. Crystallogr. 63, 32–41 (2007).

    Article  CAS  Google Scholar 

  53. Emsley, P., Lohkamp, B., Scott, W.G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).

    Article  CAS  Google Scholar 

  54. Cowtan, K. The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr. D Biol. Crystallogr. 62, 1002–1011 (2006).

    Article  Google Scholar 

  55. Smart, O.S. et al. Exploiting structure similarity in refinement: automated NCS and target structure restraints in Buster. Acta Crystallogr. D Biol. Crystallogr. 68, 368–380 (2012).

    Article  CAS  Google Scholar 

  56. Vagin, A. & Teplyakov, A. Molecular replacement with MOLREP. Acta Crystallogr. D Biol. Crystallogr. 66, 22–25 (2010).

    Article  CAS  Google Scholar 

  57. Laskowski, R.A., Mac Arthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structure. J. Appl. Crystallogr. 26, 283–291 (1993).

    Article  CAS  Google Scholar 

  58. Altschul, S.F. & Koonin, E.V. Iterated profile searches with PSI-BLAST–a tool for discovery in protein databases. Trends Biochem. Sci. 23, 444–447 (1998).

    Article  CAS  Google Scholar 

  59. Edgar, R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

    Article  CAS  Google Scholar 

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Acknowledgements

This work was supported by Association pour la Recherche contre le Cancer grant numbers 4995 and 8006 to S.B. and J.-B.C. E.G. has received a Ministère de l'Education Nationale de la Recherche et de la Technologie (University Paris Sud) and Fondation pour la Recherche Médicale PhD fellowships. We thank the European Commission Infrastructure Protein Production Platform (P-CUBE) project (FP7/2007-2013; grant no. 227764) for access to the High Throughput Crystallization platform at the Grenoble Outstation of the European Molecular Biology Laboratory (EMBL). We thank synchrotrons SOLEIL (beamline Proxima 1; Gif, France) and European Synchrotron Radiation Facility (beamlines ID29, ID23-1, ID23-2; Grenoble, France) for access to beamlines. We thank R.D. Kolodner (Ludwig Institute for Cancer Research, La Jolla, California, USA) and P. Bertrand (Commisariat à l'Energie Atomique, Fontenay-aux-Roses, France) for yeast strains and X. Veaute for help in DNA purification. We thank A. Thompson, S. Zinn-Justin and R. Guerois for careful reading of the manuscript.

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Authors and Affiliations

  1. Unité Mixte de Recherche 8221, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Institut de Biologie et Technologies de Saclay, Gif-sur-Yvette, France

    Emeric Gueneau, Carine Tellier-Lebegue, Bernard Gilquin, Pierre Bonnesoeur, Floriana Londino, Cathy Quemener, Marie-Hélene Le Du & Jean-Baptiste Charbonnier

  2. Université Paris Sud, Orsay, France

    Emeric Gueneau, Carine Tellier-Lebegue, Bernard Gilquin, Pierre Bonnesoeur, Floriana Londino, Cathy Quemener, Marie-Hélene Le Du & Jean-Baptiste Charbonnier

  3. Unité Mixte de Recherche 217, Institut de Radiobiologie Cellulaire et Moléculaire, Fontenay-aux-Roses, France

    Claudine Dherin & Serge Boiteux

  4. Unité Propre de Recherches 4301, Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique, Orléans, France

    Claudine Dherin & Serge Boiteux

  5. SOLEIL Synchrotron, L'Orme de Merisiers Saint Aubin, Gif-sur-Yvette, France

    Pierre Legrand

  6. High Throughput Crystallization Laboratory, European Molecular Biology Laboratory, Grenoble, France

    Josan A Márquez

  7. Service d'Ingénierie Moléculaire des Protéines, Commissariat à l'Energie Atomique, Institut de Biologie et Technologies de Saclay, Gif-sur-Yvette, France

    Mireille Moutiez & Muriel Gondry

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  1. Emeric Gueneau
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Contributions

S.B. and J.-B.C. designed the research; E.G., C.D., P.L., C.T.-L., B.G., P.B., F.L., C.Q., M.-H.L.D., J.A.M., M.M., M.G., S.B. and J.-B.C. carried out the experiments; E.G., C.D., P.L., C.T.-L., S.B. and J.-B.C. analyzed the data; S.B. and J.-B.C. wrote the manuscript.

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Correspondence to Serge Boiteux or Jean-Baptiste Charbonnier.

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Gueneau, E., Dherin, C., Legrand, P. et al. Structure of the MutLα C-terminal domain reveals how Mlh1 contributes to Pms1 endonuclease site. Nat Struct Mol Biol 20, 461–468 (2013). https://doi.org/10.1038/nsmb.2511

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