DNA Mismatch Repair


DNA mismatch repair is the mechanism of repairing DNA by the removal of mismatched nucleotides via MMR proteins. The role of mismatch repair proteins in the prokaryotic DNA helped to study the mismatch repair system in the eukaryotic DNA as well. The mismatch repair system is essential as it maintains the stability of the genome at the time of DNA duplication, recombination etc. The MMR system makes the use of MMR or Mismatch repair proteins to repair both the prokaryotic and eukaryotic DNA type.

In the absence of MMR system, some defect arises, which are associated with:

  • Genome instability
  • A predisposition of certain types of cancer
  • Abnormalities in meiosis cell division
  • Sterility in the mammalian system

To explain the MMR system, E.coli is the best model organism. So, in this content, we will come to know the MMR system, its components, functional role and mechanism steps.

Content: DNA Mismatch Repair

  1. Definition of DNA Mismatch Repair
  2. Types
  3. Functional Role
  4. Mechanism Steps

Definition of DNA Mismatch Repair

DNA mismatch repair can define as the rescue system that conserves the sequences of the DNA by removing the erroneous mismatched, inserted or deleted bases which arises during the DNA duplication and recombination. Mismatch repair system functions to maintain genomic stability and integrity. It reduces the chances of error by 20-400 fold in an E.coli.


The mismatch repair is generally of two types, namely:

  1. Prokaryotic MMR
  2. Eukaryotic MMR

Types of MMR

Prokaryotic Mismatch Repair

It consists of four essential components like:

prokaryotic mismatch repair

MutS: It is the most crucial protein complex whose function is to recognize the mismatched bases in the DNA. MutS protein complex is the first enzyme, which initiates the process of MMR by recognizing the non-specific sequences in the DNA. It consists of two specific sites:

  • DNA binding site: Through this site, the MutS protein complex binds to the location of DNA lesion.
  • ATPase or Dimerization site: This site brings about the conformational change in the MutS protein.

The above two sites are sterically distant from each other, as both can affect each other’s function.

MutL: It acts as an “Intermediate protein” complex which links the MutS protein and endonuclease enzyme. Thus, it is associated between the two activities (Recognition and excision of mismatched bases). MutL first binds with the activated MutS and then activates the endonuclease enzyme, i.e. MutH. MutL performs one another function, by recruiting and loading of helicase enzyme (UvrD) onto the DNA mismatched site.

MutH: It belongs to the type-II family of restriction endonucleases. MutH creates a nick in the hemimethylated GATC site. Its endonuclease activity triggers by the combination of MutS, MutL and an ATP molecule. MutH protein also consists of C-terminal, which functions as a molecular attachment site where the other two enzymes (MutS and MutL) communicates and stimulates MutH activity.

UvrD: It also refers to as “DNA helicase II” enzyme complex, which function is to unwind the DNA lesion site. MutL helps in the loading of UvrD protein onto the mismatched site and also stimulates the intrinsic helicase activity of an UvrD enzyme. The SSB proteins and UvrD enters the ss-DNA via nick created by the MutH complex.

DNA specific exonucleases: Exonuclease enzymes like Exo-I, Exo-X and 5’-3’ exonuclease performs the excision of the newly formed DNA between the nick and mismatch.

Eukaryotic Mismatch Repair

It consists of the following components like:

eukaryotic mismatch repair

MSHs protein: It shows homology with the MutS enzyme of prokaryotic MMR. In yeasts and mammals, MSH2 to MSH6 protein complexes are found. MSH enzyme is a heterodimer protein complex, which consists of two domains:

  • MutSa: It contains two types of subunits namely, MSH2 and MSH6. MSH2 contributes 80-90% of the cellular level. Msh6 recognizes the mismatched bases, particularly base-base mismatches and insertion/deletion loop as well.
  • MutSb: It contains two types of subunits namely, MSH2 and MSH3. It mainly repairs the insertion/deletion mispairs.

MLH protein: It resembles a MutL enzyme of prokaryotes MMR. MLH protein consists of four highly conserved proteins in yeasts and mammals, namely, MLH1, MLH3, PMS1 and PMS2. It also acts as a heterodimer protein complex, consists of three subunits:

  • MutLa: It consists of two subunits MLH1, PMS2. MutLa coordinates with the Mut-S complex to repair the damage.
  • MutLb: It consists of two subunits MLH1, PMS 1. MutLb functions are not known.
  • MutLg: It consists of two subunits MLH1, MLH3. MutLg repairs an insertion or deletion loop damage and involves in the meiotic division.

Accessory proteins: It includes enzymes like PCNA (Proliferating cell nuclear antigens), Recognition replication protein A (RPA), Replication factor C (RPC), Binding exonuclease-I etc.

Functional Role

DNA mismatch repair involves a simple mechanism of excising mismatched bases along with 3,000 base pairs. Other than excision of mismatched bases, it also performs certain other functions according to the recent study, like:

functional role of MMR

      1. These proteins repair the post replication repair of mismatched DNA.
      2. Promotion of meiotic cross over
      3. DNA damage response
      4. Diversification of immunoglobulins
      5. Suppression of homologous recombination by antirecombinational activity between divergent sequences

Mechanism Steps

Both the prokaryotic and eukaryotic mismatch repair involves the same basic steps to recover the mismatched DNA:

general steps of MMR

Mismatch recognition

In prokaryotic MMR: The MutS protein complex detects the DNA lesion and combines with an ATP molecule and gets activated.

In eukaryotic MMR: The MSH protein complex recognizes the non-matched bases in a DNA strand and gets activated by an ATP molecule.

Recruitment of related proteins

In prokaryotic MMR: The activated ATP-MutS complex recruits MutL, which acts as a carrier protein complex. MutS and MutL complex then activates the MutH complex. MutS, MutL and MutH form the ternary complex which loads the DNA helicase-II or UvrD enzyme onto the DNA lesion site.

In eukaryotic MMR: The activated ATP-MSH complex recruits PCNA and polymerase-δ. Then ATP dependent conformation change occurs in the mobile clamp. The conformational change recruits the binding of MutLa complex. Then, the PCNA (Proliferating cell nuclear antigens), activates the MutLa complex and creates a nick in a daughter strand.

Excision and Replacement

In prokaryotic MMR: Exonuclease-I is activated by the MutSa protein, which removes the mispaired bases. RDA protein then displaces the mismatched base. After removal of the mismatched baseS, exonuclease-I is stopped by MutSa and MutLa.

In eukaryotic MMR: The MutLa complex promotes the digestion of the mismatched bases by the exonuclease activity-I with the association of RPA (Recognition replication protein A).

Gap filling

In eukaryotic MMR: The RFC (Replication factor-C) enzyme plays an important in the synthesis of new DNA bases. Replication factor-C enzyme attaches at the 3’ primer site and activates the DNA polymerase activity to form new bases. Single stranded binding proteins (SSB) prevents the new DNA to become double-stranded. Finally, DNA ligase fills the gap in the DNA strand.

In prokaryotic MMR: The DNA polymerase III through its 5’-3’ activity forms new bases. Single stranded binding proteins (SSB) also bind to the new DNA strand and prevents the new DNA to become double-stranded. Finally, DNA ligase fills the gaps in the DNA strand.

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