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Mechanism of mismatch recognition revealed by human MutSβ bound to unpaired DNA loops

Abstract

DNA mismatch repair corrects replication errors, thus reducing mutation rates and microsatellite instability. Genetic defects in this pathway cause Lynch syndrome and various cancers in humans. Binding of a mispaired or unpaired base by bacterial MutS and eukaryotic MutSα is well characterized. We report here crystal structures of human MutSβ in complex with DNA containing insertion-deletion loops (IDL) of two, three, four or six unpaired nucleotides. In contrast to eukaryotic MutSα and bacterial MutS, which bind the base of a mismatched nucleotide, MutSβ binds three phosphates in an IDL. DNA is severely bent at the IDL; unpaired bases are flipped out into the major groove and partially exposed to solvent. A normal downstream base pair can become unpaired; a single unpaired base can thereby be converted to an IDL of two nucleotides and recognized by MutSβ. The C-terminal dimerization domains form an integral part of the MutS structure and coordinate asymmetrical ATP hydrolysis by Msh2 and Msh3 with mismatch binding to signal for repair.

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Figure 1: Overall structures of MutSβ–DNA complexes.
Figure 2: Comparison of MutSα and MutSβ proteins.
Figure 3: IDL recognition by MutSβ.
Figure 4: Dimerization domains (DMD) of MutSβ.
Figure 5: Asymmetric ATPase sites of MutSβ.
Figure 6: Mechanism of mismatch recognition.

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Acknowledgements

We thank J. Jiang for collecting X-ray diffraction data of Loop4; A. Howard for help with data processing; T. Kunkel for the term 'isomerization'; R. Kolodner, E. Alani and J. Surtees for vital discussions; and D. Leahy for critical reading of the manuscript. The research of all authors was funded by the intramural research program of the National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health.

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S.G. conducted all experiments and collected X-ray data. W.Y. determined and refined the structures. S.G., M.G. and W.Y. contributed to the experimental design, data interpretation and manuscript preparation.

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Correspondence to Wei Yang.

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Gupta, S., Gellert, M. & Yang, W. Mechanism of mismatch recognition revealed by human MutSβ bound to unpaired DNA loops. Nat Struct Mol Biol 19, 72–78 (2012). https://doi.org/10.1038/nsmb.2175

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