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DNA Mismatch Repair (MMR) occurs when a mismatch of DNA bases occurs during DNA replication that is not corrected by the polymerases. This mismatch can be at a single nucleotide or an insertion or deletion of up to 4 bases. An integral protein in MMR is MutH. MutH is an endonuclease, which means it is an enzyme that can digest DNA in the middle of the sequence. However, it is a weak endonuclease so it will only cause a single-stranded nick upstream or downstream of the damaged daughter strand DNA and not the correct parent strand. This allows it to be re-replicated as the correct sequence by DNA polymerase. Homodimers of MutS and MutL bind the mismatched DNA and create a loop that MutH can bind to. Therefore, MutS and MutL are necessary to recruit MutH to nick the DNA. In order to maintain the correct DNA sequence and repair the damaged portion without mutations, MutH must be able to differentiate the incorrect daughter strand from the correct parent strand. In bacteria, the freshly replicated DNA is hemimethylated, meaning that the parent strand is methylated and the daughter strand has not yet been methylated by methyltransferases. MutH then nicks the phosphodiester bond 5' of a GATC palindrome on the umethylated daughter strand. The GATC palindrome can be upstream or downstream of the damaged DNA site by up to 1000 nucleotides. This allows the damaged strand to be destroyed by exonucleases and re-replicated by DNA polymerase as the correct sequence.

Structure of MutH

MutH has two subdomains, the "N" arm and the "C"arm which is based on the N and C termini of the protein. These arms are arranged in a "V" shape. The N arm contains the catalytic core consisting of the DEK motif and an essential Glu56 residue. The catalytic core is where the endonuclease reaction of hydrolyzing the phosphodiester bond occurs. The DEK motif consists of Asp(D)-X(n)-Glu(E)-X-Lys(K) sequence, which contains the Mg2+ required for nicking the phosphodiester bond. The DEK motif is found in most endonucleases, which highlights its importance in catalyzing the hydrolysis of the phosphodiester bond. The C-arm is responsible for base recognition and sequence-specific binding of the DNA. The cleft in the V binds the DNA. The C-term residues help to bind the N-arm and are shown to increase DNA binding in the closed position. This allows it to have the correct shape and chemical interactions to bind the appropriate DNA substrate and catalyze the hydrolysis reaction in the correct location.

The secondary structure of Beta sheets 3/9/6 and loop 67 of arm "C" bind the GATC sequence in the major groove of the DNA. The N-arm contacts 6 nucleotides of the cleavage strand in the minor groove of the DNA. Loop C1S65 H-bonds the nitrogen of the nucleotide Ala67 to stabilize the loop. Loop 67 (residues 184-190) binds the GATC motif. The G and C are hydrogen bonded by residues Asp184/Glu91 and Lys186/Gly187. Tyr212 bonds N6 the of unmodified adenine and Pro185 interacts with methylated adenine. These specific bonds allow for the recognition of hemimethylated DNA and differentiate the parent strand from the daughter strand. Loop BC Lys48 binds the oxygens of the T’s. Also, Lys45/Asp46 interacts with the phosphate backbone to narrow the minor groove of the DNA. The active (catalytic) site on the N arm is Glu56, Asp70, Glu77, and Lys79, this makes up the DEK motif. The carboxylates (Glu/Asp) coordinate two Ca+ ions in the active site. Lys79 links the two arms of MutH and allows for the sequence-specific cutting of DNA. the reaction is catalyzed by Lys79, the 3’ phosphate of DNA that is upstream of the GATC palindrome, and the nearby metal ions to activate water for a nucleophilic attack reaction to create a single-stranded nick in the daughter strand 5' to the palindrome. Once the nick is created, the damaged daughter strand can be destroyed and re-replicated correctly from the 3' end.