Cryo-EM structure of MutL-activated MutH

Strand discrimination after mismatch recognition is the second essential step that is unique to DNA mismatch repair. MutH is a latent endonuclease that cuts the newly synthesized strand at hemi-methylated GATC sites upon activation by MutL, which acts as a signaling protein between mismatch recognition by MutS and strand discrimination by MutH. While much is known about the recognition of mismatches by MutS, little is known about the activation of strand incision by MutH. Here we present the cryo-EM structure of MutL bound to MutH on a hemi-methylated GATC site at 2.8 [A] resolution. MutL binds MutH at the back of the protein, 25 [A] away from the active site. The structure reveals that activation occurs through an allosteric pathway that acts through a push- and-pull mechanism that releases an inhibitory loop from the DNA minor groove enabling histidine 112 to pull the DNA backbone closer into the active site where a lysine 116 positions a water molecule for the nucleophilic attack at the scissile bond 5 to the GATC sequence. Thus, our structure reveals how MutL couples mismatch recognition by MutS to daughter strand discrimination by MutH.