Structural Features and Functional Dependency on ?-Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease MutL.

ABSTRACT: In early reactions of DNA mismatch repair, MutS recognizes mismatched bases and activates MutL endonuclease to incise the error-containing strand of the duplex. DNA sliding clamp is responsible for directing the MutL-dependent nicking to the newly synthesized/error-containing strand. In Bacillus subtilis MutL, the ?-clamp-interacting motif (? motif) of the C-terminal domain (CTD) is essential for both in vitro direct interaction with ?-clamp and in vivo repair activity. A large cluster of negatively charged residues on the B. subtilis MutL CTD prevents nonspecific DNA binding until ? clamp interaction neutralizes the negative charge. We found that there are some bacterial phyla whose MutL endonucleases lack the ? motif. For example, the region corresponding to the ? motif is completely missing in Aquifex aeolicus MutL, and critical amino acid residues in the ? motif are not conserved in Thermus thermophilus MutL. We then revealed the 1.35 Å-resolution crystal structure of A. aeolicus MutL CTD, which lacks the ? motif but retains the metal-binding site for the endonuclease activity. Importantly, there was no negatively charged cluster on its surface. It was confirmed that CTDs of ? motif-lacking MutLs, A. aeolicus MutL and T. thermophilus MutL, efficiently incise DNA even in the absence of ?-clamp and that ?-clamp shows no detectable enhancing effect on their activity. In contrast, CTD of Streptococcus mutans, a ? motif-containing MutL, required ?-clamp for the digestion of DNA. We propose that MutL endonucleases are divided into three subfamilies on the basis of their structural features and dependence on ?-clamp.

SUBMITTER: Fukui K 

PROVIDER: S-EPMC5016104 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature