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Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA

Abstract

DNA mismatch repair is critical for increasing replication fidelity in organisms ranging from bacteria to humans. MutS protein, a member of the ABC ATPase superfamily, recognizes mispaired and unpaired bases in duplex DNA and initiates mismatch repair. Mutations in human MutS genes cause a predisposition to hereditary nonpolyposis colorectal cancer as well as sporadic tumours. Here we report the crystal structures of a MutS protein and a complex of MutS with a heteroduplex DNA containing an unpaired base. The structures reveal the general architecture of members of the MutS family, an induced-fit mechanism of recognition between four domains of a MutS dimer and a heteroduplex kinked at the mismatch, a composite ATPase active site composed of residues from both MutS subunits, and a transmitter region connecting the mismatch-binding and ATPase domains. The crystal structures also provide a molecular framework for understanding hereditary nonpolyposis colorectal cancer mutations and for postulating testable roles of MutS.

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Figure 1: Crystal structure of the TAQ MutS–DNA complex.
Figure 2: Crystal structure of a TAQ MutS subunit.
Figure 3: Structures of the MutS dimer.
Figure 4: Mismatch recognition by MutS.
Figure 5: Structure-based sequence alignment.
Figure 6: The ‘transmitter’, HNPCC and MMR.

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References

  1. Modrich, P. & Lahue, R. Mismatch repair in replication fidelity, genetic recombination, and cancer biology. Annu. Rev. Biochem. 65, 101–133 ( 1996).

    Article  CAS  Google Scholar 

  2. Umar, A. & Kunkel, T. A. DNA-replication fidelity, mismatch repair and genome instability in cancer cells. Eur. J. Biochem. 238, 297–307 ( 1996).

    Article  CAS  Google Scholar 

  3. Human Genome Mutation Database [online] (cited 25 March 2000) 〈http://www.uwcm.ac.uk/uwcm/mg/ns/1/203983.html〉 (1997).

  4. HNPCC Mutation Database [online] (cited 25 March 2000) 〈http://www.nfdht.nl/database/msh2.htm〉 ( 1997).

  5. Herman, J. G. et al. Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma. Proc. Natl Acad. Sci. USA 95, 6870–6875 (1998).

    Article  ADS  CAS  Google Scholar 

  6. 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 

  7. Jiricny, J. Eukaryotic mismatch repair: an update. Mutat. Res. 409, 107–121 (1998).

    Article  CAS  Google Scholar 

  8. Allen, D. J. et al. MutS mediates heteroduplex loop formation by a translocation mechanism. EMBO J. 14, 4467– 4476 (1997).

    Article  Google Scholar 

  9. Biswas, I. et al. Oligomerization of a MutS mismatch repair protein from Thermus aquaticus. JBC 274, 23673– 23678 (1999).

    Article  CAS  Google Scholar 

  10. Buermeyer, A. B., Deschênes, S. M., Baker, S. M. & Liskay, R. M. Mammalian DNA mismatch repair. Annu. Rev. Genet. 33 , 533–564 (1999).

    Article  CAS  Google Scholar 

  11. Eisen, J. A. A phylogenomic study of the MutS family of proteins. Nucleic Acids Res. 26, 4291–4300 ( 1998).

    Article  CAS  Google Scholar 

  12. Matic, I., Taddei, F. & Radman, M. Genetic barriers among bacteria. Trends Microbiol. 4, 69–72 (1996 ).

    Article  CAS  Google Scholar 

  13. Nakagawa, T., Datta, A. & Kolodner, R. Multiple functions of MutS- and MutL-related heterocomplexes. Proc. Natl Acad. Sci. USA 96, 14186– 14188 (1999).

    Article  ADS  CAS  Google Scholar 

  14. Gradia, S., Acharya, S. & Fishel, R. The human mismatch recognition complex hMSH2-hMSH6 functions as a novel molecular switch. Cell 91, 995 –1005 (1997).

    Article  CAS  Google Scholar 

  15. Alani, E., Sokolsky, T., Studamire, B., Miret, J. J. & Lahue, R. S. Genetic and biochemical analysis of Msh2p-Msh6p: role of ATP hydrolysis and Msh2p-Msh6p subunit interactions in mismatch base pair recognition. Mol. Cell. Biol. 17, 2436–2447 (1997).

    Article  CAS  Google Scholar 

  16. Bjornson, K. P., Allen, D. J. & Modrich, P. Modulation of MutS ATP hydrolysis by DNA cofactors. Biochemistry 39, 3176– 3183 (2000).

    Article  CAS  Google Scholar 

  17. Su, S. S. & Modrich, P. Escherichia coli mutS-encoded protein binds to mismatched DNA base pairs. Proc. Natl Acad. Sci. USA 83, 5057–5061 ( 1986).

    Article  ADS  CAS  Google Scholar 

  18. Haber, L. T. & Walker, G. C. Altering the conserved nucleotide binding motif in the Salmonella typhimurium MutS mismatch repair protein affects both its ATPase and mismatch binding activities. EMBO J. 10, 2707–2715 ( 1991).

    Article  CAS  Google Scholar 

  19. Biswas, I. & Hsieh, P. Identification and characterization of a thermostable MutS homolog from Thermus aquaticus. J. Biol. Chem. 271, 5040–5048 (1996).

    Article  CAS  Google Scholar 

  20. Hendrickson, W. A., Horton, J. R. & LeMaster, D. M. Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J. 9, 1665–1672 (1990).

    Article  CAS  Google Scholar 

  21. Yang, W. & Steitz, T. A. Recombining the structures of HIV integrase, RuvC and RNase H. Structure 3, 131–134 (1995).

    Article  CAS  Google Scholar 

  22. Gorbalenya, A. E. & Koonin, E. V. Superfamily of UvrA-related NTP-binding proteins implication for rational classfication of recombination /repair systems. J. Mol. Biol. 213 , 583–591 (1990).

    Article  CAS  Google Scholar 

  23. Hung, L. -W. et al. Crystal structure of the ATP-binding subunit of an ABC transporter. Nature 396, 703–707 (1998).

    Article  ADS  CAS  Google Scholar 

  24. Berger, J. M. & Wang, J. C. Recent developments in DNA topoisomerase II structure and mechanism. Curr. Opin. Struct. Biol. 6, 84–90 (1996).

    Article  CAS  Google Scholar 

  25. Jones, M., Wagner, R. & Radman, M. Repair of a mismatch is influenced by the base composition of the surrounding nucleotide sequence. Genetics 115 , 605–610 (1987).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Malkov, V. A., Biswas, I., Camerini-Otero, R. D. & Hsieh, P. Photocross-linking of the NH2-terminal region of Taq MutS protein to the major groove of a heteroduplex DNA. J. Biol. Chem. 272, 23811–23817 (1997).

    Article  CAS  Google Scholar 

  27. Biswas, I. & Hsieh, P. Interaction of MutS protein with the major and minor grooves of a heteroduplex DNA. J. Biol. Chem. 272, 23811–23817 (1997).

    Article  Google Scholar 

  28. Bajski, S. R., Jackson, B. A. & Barton, J. K. DNA repair: models for damage and mismatch recognition. Mutat. Res. 447, 49–72 (2000).

    Article  Google Scholar 

  29. Ohndorf, U. M., Rould, M. A., He, Q., Pabo, C. O. & Lippard, S. J. Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins. Nature 399, 708–712 (1999).

    Article  ADS  CAS  Google Scholar 

  30. Dickerson, R. E. DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Res. 26, 1906–1926 (1998).

    Article  CAS  Google Scholar 

  31. Bowers, J., Sokolsky, T., Quach, T. & Alani, E. A mutation in the MSH6 subunit of the Saccharomyces cerevisiae MSH2-MSH6 complex disrupts mismatch recognition. J. Biol. Chem. 274, 16115–16125 (1999).

    Article  CAS  Google Scholar 

  32. Das Gupta, R. & Kolodner, R. D. Novel dominant mutations in Saccharomyces cerevisiae MSH6. Nature Genet. 24 , 53–56 (2000).

    Article  CAS  Google Scholar 

  33. Holland, I. B. & Blight, M. A. ABC-ATPases, adaptable energy generators fuelling transmembrane movement of a variety of molecules in organisms from bacteria to humans. J. Mol. Biol. 293, 381–399 (1999).

    Article  CAS  Google Scholar 

  34. Hopfner, K. P. et al. Structural biology of Rad50 ATPase: ATP-driven conformational control in DNA double-strand break repair and the ABC-ATPase superfamily. Cell 101, 789–800 (2000).

    Article  CAS  Google Scholar 

  35. Zalevsky, J., MacQueen, A. J., Duffy, J. B., Kemphues, K. J. & Villeneuve, A. M. Crossing over during Caenorhabditis elegans meiosis requires a conserved MutS-based pathway that is partially dispensable in budding yeast. Genetics 153, 1271–1283 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Studamire, B., Price, G., Sugawara, N., Haber, J. E. & Alani, E. Separation-of-function mutations in Saccharomyces cerevisiae MSH2 that confer mismatch repair defects but do not affect nonhomologous-tail removal during recombination. Mol. Cell. Biol. 19, 7558–7567 ( 1999).

    Article  CAS  Google Scholar 

  37. Gradia, S. et al. hMSH2-hMSH6 forms a hydrolysis-independent sliding clamp on mismatch DNA. Mol. Cell 3, 255– 261 (1999).

    Article  CAS  Google Scholar 

  38. Grilley, M., Welsh, K. M., Su, S. -S. & Modrich, P. Isolation and characterization of the Escherichia coli mutL gene product. J. Biol. Chem. 264, 1000– 1004 (1989).

    CAS  PubMed  Google Scholar 

  39. Habraken, Y., Sung, P., Prakash, L. & Prakash, S. ATP-dependent assembly of a ternary complex consisting of a DNA mismatch and the yeast MSH2-MSH6 and MLH1-PMS1 protein complexes. J. Biol. Chem. 273, 9837–9841 (1998).

    Article  CAS  Google Scholar 

  40. Ban, C. & Yang, W. Structural basis for MutH activation in E. coli mismatch repair and relationship of MutH to restriction endonucleases. EMBO J. 17, 1526– 1534 (1998).

    Article  CAS  Google Scholar 

  41. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 ( 1997).

    Article  CAS  Google Scholar 

  42. Terwilliger, T. C. SOLVE: An automated structure solution for MAD and MIR. Edition 1.16 [online] 〈http://www.solve.lanl.gov〉 (1997).

  43. CCP4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994).

    Article  Google Scholar 

  44. Jones, T. A., Zou, J. -Y. & Cowan, S. W. Improved methods for building models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 ( 1991).

    Article  Google Scholar 

  45. Brünger, A. T. et al. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998).

    Article  Google Scholar 

  46. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and themodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281–296 ( 1991).

    Article  CAS  Google Scholar 

  47. Carson, M. Ribbon models of macromolecules. J. Mol. Graphics 5 , 103–106 (1987).

    Article  CAS  Google Scholar 

  48. Drotschmann, K., Clark, A. B. & Kunkel, T. A. Mutator phenotypes of common polymorphisms and missense mutations in MSH2. Curr. Biol. 9, 907– 910 (1999).

    Article  CAS  Google Scholar 

  49. Drotschmann, K. et al. Mutator phenotypes of yeast strains heterozygous for mutations in the MSH2 gene. Proc. Natl Acad. Sci. USA 96, 2970–2975 (1999).

    Article  ADS  CAS  Google Scholar 

  50. Wu, T. -H. & Marinus, M. G. Dominant negative mutator mutations in the mutS gene of Escherichia coli. J. Bacteriol. 176, 5393–5400 ( 1994).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank I. Biswas for TAQ MutS expression vectors; Z. Dauter and C. Ogata for synchrotron beamline support; G. Poy for oligonucleotide synthesis; Q. Zhao for assistance in data collection; E. Alani, D. Camerini-Otero, R. Craigie, M. Gellert, M. Junop, T. Kunkel, D. Leahy, K. Mizuuchi, H. Nash and M. Radman for discussions and comments on the manuscript.

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Correspondence to Wei Yang.

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Obmolova, G., Ban, C., Hsieh, P. et al. Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA. Nature 407, 703–710 (2000). https://doi.org/10.1038/35037509

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