Asymmetric ATP Binding and Hydrolysis Activity of the Thermus aquaticus MutS Dimer Is Key to Modulation of Its Interactions with Mismatched DNA

Abstract

Prokaryotic MutS and eukaryotic Msh proteins recognize base pair mismatches and insertions or deletions in DNA and initiate mismatch repair. These proteins function as dimers (and perhaps higher order oligomers) and possess an ATPase activity that is essential for DNA repair. Previous studies of Escherichia coli MutS and eukaryotic Msh2-Msh6 proteins have revealed asymmetry within the dimer with respect to both DNA binding and ATPase activities. We have found the Thermus aquaticus MutS protein amenable to detailed investigation of the nature and role of this asymmetry. Here, we show that (a) in a MutS dimer one subunit (S1) binds nucleotide with high affinity and the other (S2) with 10-fold weaker affinity, (b) S1 hydrolyzes ATP rapidly while S2 hydrolyzes ATP at a 30-50-fold slower rate, (c) mismatched DNA binding to MutS inhibits ATP hydrolysis at S1 but slow hydrolysis continues at S2, and (d) interaction between mismatched DNA and MutS is weakened when both subunits are occupied by ATP but remains stable when S1 is occupied by ATP and S2 by ADP. These results reveal key MutS species in the ATPase pathway; S1 ADP -S2 ATP is formed preferentially in the absence of DNA or in the presence of fully matched DNA, while S1 ATP -S2 ATP and S1 ATP -S2 ADP are formed preferentially in the presence of mismatched DNA. These MutS species exhibit differences in interaction with mismatched DNA that are likely important for the mechanism of MutS action in DNA repair.Mismatch repair maintains genomic integrity by correcting mispaired bases and insertions or deletions that occur in DNA due to errors in DNA replication or recombination. The process initiates with a mismatch recognition phase, in which MutS protein binds to the distortion in the DNA duplex, followed by excision of the offending DNA strand, catalyzed by helicase and exonuclease enzymes, and finally DNA resynthesis and ligation of the new strand, apparently by the normal DNA replication machinery (1). In Escherichia coli, after MutS (a homodimer) binds the mismatch, it interacts with MutL (also a homodimer), resulting in stimulation of MutH endonuclease activity and nicking of the mismatch-containing DNA strand to initiate strand excision (2-4). Since these core components of the DNA mismatch repair system were identified in E. coli, homologues of MutS and MutL have been discovered and analyzed in numerous other organisms, including humans. Eukaryotic MutS proteins function as heterodimers, such as Msh2-Msh6, 1 which recognizes base pair mismatches and small insertion or deletion loops, and Msh2-Msh3, which appears to be specific for insertion or † This work was supported by a grant from the N. .

Contribution of Msh2 and Msh6 subunits to the asymmetric ATPase and DNA mismatch binding activities of Saccharomyces cerevisiae Msh2–Msh6 mismatch repair protein

“…Amino acids from each MutS subunit make distinctly different, sequence-independent contacts with mismatched DNA, and only one subunit uses a Phe-XGlu motif for base-specific stacking and hydrogen bonding interactions with the mismatch [22,23,34]. Both subunits bind ATP, but with differing affinities, and their ATPase kineics are also very different [18][19][20][21]. Since prokaryotic MutS is a homodimer, it is not clear whether the asymmetry is an intrinsic property of the protein itself, or whether it arises following MutS interaction with nucleotide and/or DNA.…”

“…Phosphate (P i ) release assays were performed on an SF-2001 stopped-flow instrument (KinTek Corp., Austin, TX) as described [18]. Briefly, 60 μl of 4μM Msh2-Msh6 (±6μM DNA) and 16 μM MDCC-PBP was mixed with 60μl of 1 mM ATP (final concentrations: 2 μM Msh2-Msh6, 8 μM MDCC-PBP, 500 μM ATP, and 3 μM DNA).…”

“…In fact it appears that the asymmetry in the ATPase sites is linked to asymmetry in the interactions of the two subunits with DNA [24,25]. Consistent with this hypothesis, binding of mismatched DNA to MutS specifically suppresses the catalytic activity of the high-affinity subunit, such that the rate of ATP hydrolysis is reduced from 10 to 0.3 s −1 [18]. The exact nature and function of asymmetry in the MutS dimer is not clear as yet, but the characteristic appears to be important for DNA mismatch repair as it is conserved among a variety of organisms.…”

“…Recent studies from several research groups, including our own, have revealed clear differences between the ATP binding and hydrolysis activities of the two subunits in the MutS/Msh dimer [18][19][20][21]. For instance, in Thermus aquaticus MutS, one subunit binds nucleotide (ATPγS) with about 10-fold higher affinity than the other subunit (K D = 3μM versus 27μM).…”

“…For instance, in Thermus aquaticus MutS, one subunit binds nucleotide (ATPγS) with about 10-fold higher affinity than the other subunit (K D = 3μM versus 27μM). Also, the high-affinity subunit hydrolyzes ATP at >30-fold faster rate than the low-affinity subunit (10 s −1 versus 0.2-0.3 s −1 at 40 °C) [18]. These differences are striking especially since MutS is a homodimer; however, they are in accord with known differences in the DNA binding activities of the two MutS subunits (e.g., conserved phenylalanine and glutamate residues from only one subunit undergo base stacking and hydrogen bonding interactions with the mismatch, respectively) [22,23].…”