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43  structures 7009  species 0  interactions 11775  sequences 118  architectures

Family: DNA_mis_repair (PF01119)

Summary: DNA mismatch repair protein, C-terminal domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "DNA mismatch repair". More...

DNA mismatch repair Edit Wikipedia article

Mismatch Repair

The cell requires a means of repairing mismatches that occur between base pairs during replication – for example, if a guanine nucleotide (G) is paired with a thymine (T), or an adenine (A) is paired with a cytosine (C) (see DNA repair). Therefore, cells have an entire mismatch repair system that replaces mismatched bases in newly synthesized daughter strands by first cleaving off the damage and then inserting the correct nucleotides.

Mut Proteins

The Mut proteins are the major players in the mismatch repair system. MutS recognizes the mismatched base on the daughter strand and binds the mutated DNA. It is then joined by MutL, which binds the MutS-DNA complex. MutL activates the endonuclease MutH, which incises the daughter strand near the mismatch with the help of the helicase UvrD. An exonuclease then digests the nicked strand, moving in the direction of the mismatch, and ending past the mismatch site. Which exonuclease is used is dependent on which side of the mismatch MutH incises the strand – 5’ or 3’. If the nick is on the 5’ end of the mismatch, either RecI or exonuclease VIII, both 5’ to 3’ exonucleases, are used; if however, MutH nicks on the 3’ end of the mismatch, the 3’ to 5’ exonuclease I is used. These exonucleases create a single-stranded gap that can be repaired by DNA Polymerase III, which uses the other strand as a template, and sealed by DNA ligase.

Choosing the Right Strand

The question arises as to how MutS knows which strand is the daughter strand and therefore contains the incorrect base, for replacing the base on the parent strand would result in an undesired mutation. In E.coli, the solution lies in hemimethylation, for as the daughter strand is unmethylated, the repair system can distinguish between the two strands. MutH actually binds at hemimethylated sites along DNA, but its action is latent, being activated only upon contact by MutL. Upon activation, MutH can perform its cleavage selectively on the unmethylated daughter strand.

External Links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

DNA mismatch repair protein, C-terminal domain Provide feedback

This family represents the C-terminal domain of the mutL/hexB/PMS1 family. This domain has a ribosomal S5 domain 2-like fold.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013507

This domain is found in MutL and homologues and is characterized by a ribosomal protein S5 domain 2-like fold [ PUBMED:26249686 ].

The dimeric MutL protein has a key function in communicating mismatch recognition by MutS to downstream repair processes. Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex [ PUBMED:14527292 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan S5 (CL0329), which has the following description:

This superfamily contains a wide range of families that possess a structure similar to the second domain of ribosomal S5 protein.

The clan contains the following 18 members:

ChlI DNA_gyraseB DNA_mis_repair EFG_IV Fae GalKase_gal_bdg GHMP_kinases_N IGPD Lon_C LpxC Morc6_S5 Ribonuclease_P Ribosomal_S5_C Ribosomal_S9 RNase_PH Topo-VIb_trans UPF0029 Xol-1_N


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

Representative proteomes UniProt
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

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Representative proteomes UniProt

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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

Representative proteomes UniProt
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: SCOP
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A , Griffiths-Jones SR
Number in seed: 113
Number in full: 11775
Average length of the domain: 120.1 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 16.3 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.0 26.0
Trusted cut-off 26.1 26.0
Noise cut-off 25.9 25.9
Model length: 119
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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The tree shows the occurrence of this domain across different species. More...


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the DNA_mis_repair domain has been found. There are 43 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044S314 View 3D Structure Click here
A0A077Z6K9 View 3D Structure Click here
A0A077ZC15 View 3D Structure Click here
A0A0D2DME9 View 3D Structure Click here
A0A0D2GLW7 View 3D Structure Click here
A0A0D2HFX7 View 3D Structure Click here
A0A0H3GMA2 View 3D Structure Click here
A0A0H5S2C1 View 3D Structure Click here
A0A0K0E0I8 View 3D Structure Click here
A0A0K0EEM3 View 3D Structure Click here
A0A0N4U1Z4 View 3D Structure Click here
A0A0N4U910 View 3D Structure Click here
A0A150AST9 View 3D Structure Click here
A0A175W396 View 3D Structure Click here
A0A1C1C7P3 View 3D Structure Click here
A0A1C1CKC1 View 3D Structure Click here
A0A1C1CXY5 View 3D Structure Click here
A0A1D6EUN3 View 3D Structure Click here
A0A1D6Q3Y5 View 3D Structure Click here
A0A1D8PII6 View 3D Structure Click here
A0A1Y7VMP7 View 3D Structure Click here
A0A2K6WG30 View 3D Structure Click here
A0A3P7FEW0 View 3D Structure Click here
A0A5K4E9D9 View 3D Structure Click here
A0A5K4FBF1 View 3D Structure Click here
A0A5S6PMW4 View 3D Structure Click here
A0B977 View 3D Structure Click here
A0KGR9 View 3D Structure Click here
A0LJK2 View 3D Structure Click here
A0Q0M7 View 3D Structure Click here
A1AT89 View 3D Structure Click here
A1BCW2 View 3D Structure Click here
A1SA23 View 3D Structure Click here
A1SZL2 View 3D Structure Click here
A1UU01 View 3D Structure Click here
A1Z7C1 View 3D Structure Click here
A1ZA03 View 3D Structure Click here
A2SSN1 View 3D Structure Click here
A3CR14 View 3D Structure Click here
A3QAD8 View 3D Structure Click here