Human MutLalpha: the jack of all trades in MMR is also an endonuclease

Abstract

Recently, Paul Modrich's group reported the discovery of an intrinsic endonuclease activity for human MutLalpha. This breakthrough provides a satisfactory answer to the longstanding puzzle of a missing nuclease activity in human mismatch repair and will undoubtedly lead to new investigations of DNA repair and replication. Here, the implications of this exciting new finding are discussed in the context of mismatch repair in Escherichia coli and humans.

Figure 1

Diagrams of the initial incision step of MMR in E.coli and humans. A. In E. coli, MutS recognizes a mismatch, binds it and bends the DNA by 60° towards the major groove. The newly synthesized and unmethylated daughter strand is shown in grey. In the presence of ATP, MutL is recruited to the MutS-mismatch complex, and together they activate MutH to nick the daughter strand on either the 5′ or 3′ side of the mismatch. Since the DNA binding activity of MutL is not necessary for this step and slightly inhibits MutH activation [34], we propose that the DNA in between the mismatch and incision site is looped out. B. In humans, MutSα is made of MSH2 (green) and MSH6 (blue) and interacts with PCNA (purple). The daughter strand is marked by a pre-existing strand break. A break 3′ to the mismatch is shown here as an example. MutSα may have a strand preference when loaded by PCNA. The ensuing MutSα-MutLα-mismatch complex could also be biased due to the asymmetric (heterodimeic) nature. Incisions by the PMS2 subunit of MutLα on the 3′ side of the mismatch may be guided by PCNA and MutSα, and incisions on the 5′ side may be limited by how far the C-terminal domain of MutLα (the endonuclease active site) can extend from the MutSα-MutLα complex located on the mismatch site.

Figure 2

Structural model of MutLα. A. A model of the C-terminal domain of PMS2 based on the E. coli MutL structure [8] (PDB accession: 1X9Z). The DQHA(X)₂E(X)₄E and CXHGRP motifs are highlighted in the ribbon diagram and written out above the diagram in the same color. B. The overall structure of an MutL dimer. The C-terminal domains of MutL form a stable dimer in E. coli and humans. The N-terminal ATPase domains associate in the presence of ATP and dissociate in its absence. The linker between the two domains contains ∼100-300 residues and adopts a rather extended conformation in E. coli MutL. Both the N- and C-terminal domains of E. coli and yeast MutL have been shown to interact with DNA. The DNA-binding region in the C-terminal domain of E. coli MutL coincides with the divalent cation-binding site in PMS2. Since MLH1 has no metal ion-binding site, MutLα is predicted to contain a single endonuclease active site. Homodimeric bacterial MutL proteins may have two endonuclease active sites per molecule, but the endonuclease activity may be asymmetric upon association with MutS and a mismatch site.