Structure of the MutL C-terminal domain: a model of intact MutL and its roles in mismatch repair

Abstract

MutL assists the mismatch recognition protein MutS to initiate and coordinate mismatch repair in species ranging from bacteria to humans. The MutL N-terminal ATPase domain is highly conserved, but the C-terminal region shares little sequence similarity among MutL homologs. We report here the crystal structure of the Escherichia coli MutL C-terminal dimerization domain and the likelihood of its conservation among MutL homologs. A 100-residue proline-rich linker between the ATPase and dimerization domains, which generates a large central cavity in MutL dimers, tolerates sequence substitutions and deletions of one-third of its length with no functional consequences in vivo or in vitro. Along the surface of the central cavity, residues essential for DNA binding are located in both the N- and C-terminal domains. Each domain of MutL interacts with UvrD helicase and is required for activating the helicase activity. The DNA-binding capacity of MutL is correlated with the level of UvrD activation. A model of how MutL utilizes its ATPase and DNA-binding activities to mediate mismatch-dependent activation of MutH endonuclease and UvrD helicase is proposed

DNA mismatch repair: Molecular mechanism, cancer, and ageing

“…In contrast to E. coli MutL, the N-terminal fragment of hPMS2 remains a monomer in the crystal structure, even in the presence of ATP, and the monomeric fragment is capable of ATP hydrolysis (Guarne et al, 2001). A crystal structure of a C-terminal dimerization domain of E. coli MutL reveals a V-shaped dimer that plays critical roles in the activation of UvrD by MutL and in DNA binding by MutL (Guarne et al, 2004). The DNA binding activity of MutL has been shown to be essential for methyl-directed MMR in E. coli (Robertson et al, 2006a).…”

Human MutLα: The jack of all trades in MMR is also an endonuclease

“…Interestingly, the substitution within the DQHA(X) 2 E(X) 4 E motif of E. coli MutL includes two Arg residues, and these Arg sidechains were shown to be important for DNA binding (Fig. 2B) [8]. In the modeled PMS2 structure, the DQHA(X) 2 E(X) 4 E motif is juxtaposed to another sequence motif, CXHGRP, conserved among hPMS2-like MutL homologs ( Fig.…”

“…This conserved motif is mapped onto an exposed surface of the C-terminal domain based on the crystal structure of the E. coli protein ( Fig. 2A) since all MutL homologs are predicted to have a conserved tertiary fold [8,9]. Interestingly, the substitution within the DQHA(X) 2 E(X) 4 E motif of E. coli MutL includes two Arg residues, and these Arg sidechains were shown to be important for DNA binding (Fig.…”

“…In the modeled PMS2 structure, the DQHA(X) 2 E(X) 4 E motif is juxtaposed to another sequence motif, CXHGRP, conserved among hPMS2-like MutL homologs ( Fig. 2A) [8,9]. Although the overall structure and arrangement of the conserved residues in hPMSs do not immediately resemble any known nucleases, conserved Cys, His, Asp and Glu residues in this region can readily form a metal ion-binding site.…”

“…To avoid non-mismatch-dependent activation, the MutH endonuclease activity needs to be negatively regulated. Both SeqA and the Dam methylase in E. coli bind and compete for hemimethylated GATC with much lower K d 's (nM) than that of MutH (μM) [8,[18][19][20][21]. They likely prevent MutH from accessing the newly synthesized daughter strand in the absence of a mismatch.…”