Distinct nucleotide binding/hydrolysis properties and molar ratio of MutSα and MutSβ determine their differential mismatch binding activities

Abstract

MutSα (MSH2/MSH6) and MutSβ (MSH2/MSH3) are eukaryotic mismatch recognition proteins that preferentially process base-base and small insertion/deletion (ID) mispairs, respectively, despite the fact that cells contain a MutSα:MutSβ ratio of 10:1. To explore the mechanism underlying the differential mismatch recognition by these two proteins, purified human MutSα and MutSβ were analyzed individually and competitively for their abilities to interact with a T-G and an ID substrate. We show that MutSα has KD values of 26.5 and 38.2 nM for the G-T and ID substrates, respectively, and that MutSβ has KD values of 76.5 and 23.5 nM for G-T and ID, respectively. Consistent with these results, competitive binding assays revealed the following relative binding affinities: MutSβ-ID > MutSα-T-G > MutSα-ID ≫ α MutSβ-T-G. Interestingly, binding of MutSβ to ID heteroduplexes is greatly stimulated when the MutSα:MutSβ ratio is ≥10. Distinct ATP/ ADP binding and ATPase activities of MutSα and MutSβ were also observed. In the absence of DNA, ADP binding and ATPase activities of MutSβ are significantly higher than those of MutSα. However, interaction with DNA significantly stimulates the MutSα ATPase activity and reduces the MutSβ ATPase activity, the consequence being that both proteins exhibit the same level of hydrolytic activity. We conclude that the preferential processing of base-base and ID heteroduplexes by MutSα and MutSβ is determined by their significant differences in ATPase activity, ADP binding activity, and high cellular MutSα:MutSβ ratio. © 2009 by The American Society for Biochemistry and Molecular Biology, Inc.