MSH3

Crystal structure of MSH2:MSH3 heterodimer in complex with DNA (PDB: 3THX​). MSH2 and MSH3 bind to form MutSβ. This crystal structure shows MutSβ bound to DNA containing an insertion loop of three unpaired nucleotides.

MSH3
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 3THW, 3THX, 3THY, 3THZ
Identifiers
Aliases	MSH3, DUP, MRP1, mutS homolog 3, FAP4
External IDs	OMIM: 600887; MGI: 109519; HomoloGene: 1829; GeneCards: MSH3; OMA:MSH3 - orthologs
Gene location (Human) Chr. Chromosome 5 (human) Band 5q14.1 Start 80,654,652 bp End 80,876,815 bp
Gene location (Mouse) Chr. Chromosome 13 (mouse) Band 13 C3|13 47.63 cM Start 92,348,380 bp End 92,491,511 bp
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in bronchial epithelial cell mucosa of paranasal sinus secondary oocyte cardia gonad testicle renal medulla external globus pallidus subthalamic nucleus Achilles tendon Top expressed in zygote tail of embryo spermatocyte secondary oocyte genital tubercle primary oocyte ventricular zone epiblast spermatid neural layer of retina More reference expression data BioGPS More reference expression data
Gene ontology Molecular function nucleotide binding DNA binding protein homodimerization activity mismatched DNA binding dinucleotide insertion or deletion binding oxidized purine DNA binding single-stranded DNA binding protein binding enzyme binding dinucleotide repeat insertion binding ATP binding single guanine insertion binding guanine/thymine mispair binding Y-form DNA binding heteroduplex DNA loop binding double-strand/single-strand DNA junction binding damaged DNA binding ATP-dependent activity, acting on DNA single thymine insertion binding DNA insertion or deletion binding Cellular component MutSbeta complex membrane nucleoplasm nucleus mismatch repair complex Biological process cellular response to DNA damage stimulus maintenance of DNA repeat elements positive regulation of helicase activity negative regulation of DNA recombination DNA mismatch repair DNA repair somatic recombination of immunoglobulin gene segments meiotic mismatch repair removal of nonhomologous ends mitotic recombination reciprocal meiotic recombination replication fork arrest Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 4437 17686 Ensembl ENSG00000113318 ENSMUSG00000014850 UniProt P20585 P13705 RefSeq (mRNA) NM_002439 NM_010829 NM_001311120 RefSeq (protein) NP_002430 NP_001298049 NP_034959 Location (UCSC) Chr 5: 80.65 – 80.88 Mb Chr 13: 92.35 – 92.49 Mb PubMed search
Wikidata
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DNA mismatch repair protein, MutS Homolog 3 (MSH3) is a human homologue of the bacterial mismatch repair protein MutS that participates in the mismatch repair (MMR) system. MSH3 typically forms the heterodimer MutSβ with MSH2 in order to correct long insertion/deletion loops and base-base mispairs in microsatellites during DNA synthesis. Deficient capacity for MMR is found in approximately 15% of colorectal cancers, and somatic mutations in the MSH3 gene can be found in nearly 50% of MMR-deficient colorectal cancers.

Gene and expression

In humans, the encoding gene for MSH3 is found on chromosome 5 at location 5q11-q12 upstream of the dihydrofolate reductase (DHFR) gene. MSH3 is encoded by 222,341 base pairs and creates a protein consisting of 1137 amino acids.

MSH3 is typically expressed at low levels in several transformed cell lines—including HeLa, K562, HL-60, and CEM—as well as a large range of normal tissues including spleen, thymus, prostate, testis, ovary, small intestine, colon, peripheral blood leukocytes, heart, brain, placenta, lung, liver, skeletal muscle kidney, and pancreas. Although expression levels of MSH3 vary slightly from tissue to tissue, its widespread low-level expression indicates that it is a “housekeeping” gene commonly expressed in all cells.

Over-expression of MSH3 decreased capacity for MMR. When MSH3 is over expressed, drastic changes occur in the relative levels of formation of MutSβ at the expense of MutSα. MutSα is responsible for base-base mispairs and short insertion/deletion loops, while MutSβ repairs long insertion/deletion loops in DNA. A drastic shift in the relative levels of these protein complexes can lead to diminished capacity for MMR. In the case of MSH3 overexpression, MSH2 preferentially heterodimerizes with MSH3 leading to high levels of MutSβ and degradation of the partnerless MSH6 protein which normally complexes with MSH2 to form MutSα.

Interactions

MSH3 has been shown to interact with MSH2, PCNA, and BRCA1. These interactions form protein complexes that are typically involved in tumor suppression and DNA repair activities.

The primary interaction of MSH3 involves forming the MutSβ complex with MSH2. MutSβ forms as a heterodimer of MSH2 and MSH3 with two primary interaction regions: an amino-terminal region and a carboxy-terminal region. The N-terminal region of MSH3 (amino acids 126-250) contact the N-terminal region of MSH2 aa 378-625. The C-terminal regions connect at aa 1050-1128 of MSH3 and aa 875-934 of MSH2. The binding regions on MSH2 are identical when binding to either MSH3 or MSH6. Adenine nucleotide binding regions in MSH3 and MSH2 are not contained in either of the interaction regions involved in dimerization, allowing MutSβ to bind to DNA and perform MMR.

External image

MutSβ Binding sites for MSH3 and MSH2 Model of the hMSH2 consensus interaction with hMSH3 or hMSH6. The interaction regions of hMSH2 with hMSH3 and of hMSH2 with hMSH6 are shown in gray and they are connected with lines that illustrate the specificity of each region to their pairing partner. The nucleotide binding regions are shown as black boxes. The location of the HNPCC mutations tested in these studies are illustrated as black diamonds. The N-terminal region of MSH3 (amino acids 126-250) contact the N-terminal region of MSH2 aa 378-625. The C-terminal regions connect at aa 1050-1128 of MSH3 and aa 875-934 of MSH2. The binding regions on MSH2 are identical when binding to either MSH3 or MSH6.

Proliferating cell nuclear antigen (PCNA) is a protein involved in post-replication MMR. It has been shown that PCNA binds to the MutSβ heterodimer via a binding motif in the N-terminal domain of MSH3. Bound PCNA then localizes the MutSβ complex to replication foci, indicating that PCNA assists in initiating repair by guiding MutSβ and other repair proteins to free termini in recently replicated DNA.

Function

The primary function of MSH3 is to maintain the stability of the genome and enact tumor suppression by forming the heterodimer MutSβ to correct long insertion/deletion loops and base-base mispairs. In the case of long insertion/deletion loops, DNA is severely bent and downstream basepairs can become unpaired and exposed. MutSβ recognizes insertion/deletion loops of 1-15 nucleotides; binding to insertion/deletion loops is achieved by inserting the mismatch-binding domain of MSH3 and part of the mismatch-binding domain of MSH2 into the groove formed by the extreme bend in DNA formed by the insertion/deletion loop.

External image

IDL recognition by MutSβ. (a) A close-up comparison of MSH3—IDL interaction and Taq MutS with a single unpaired base (ΔT). (b) DNA-binding domains and DNA in Loop4. Domains I and IV of MSH2 are shown in green and yellow, and MBD and clamp domains of MSH3 in blue and orange. (c) Diagram of the protein-DNA interactions using the same color scheme as in (b). (d) Space-filling model of four IDLs and their interaction with domain I of MSH2 (green) and MBD of MSH3 (blue). The base pairs surrounding the IDL are shown in light (upstream) and dark (downstream) pink. For Loop2 and Loop4, a back view looking into the minor groove is also shown.

Role in Cancer

The most significant role of MSH3 in cancer is the suppression of tumors by repair of somatic mutations in DNA that occur as the result of base-base mispairs and insertion/deletion loops. Both loss of expression and over expression of MSH3 can lead to carcinogenic effects.

Over-expression of MSH3 can lead to drastic changes in the relative e levels of MutSα and MutSβ. Normally, MutSβ is expressed at relatively low levels throughout all cells while MutSα is present at high levels. While both proteins have redundant function in base-base repairs, MutSα typically effects base-base mispair repairs and also performs repairs on the more common short inertion/deletion loops. When MSH3 is heavily overexpressed, it acts as a sequester for MSH2 and the relative levels of MutSβ and MutSα shift dramatically as unpaired MSH6 proteins degrade and MutSα becomes depleted. MutSβ can compensate somewhat for loss of base-base mispair correction functions, but is not suited for repairing many short, 1-2 base pair insertion/deletion loops. This leads to a heightened rate of microsatellite instabilities and increased rates of somatic mutations.

This effect is directly related to human cancer in the form of drug resistance. One of the common resistance responses to methotrexate, a drug commonly used to treat childhood acute lymphocytic leukemia and a variety of other tumors, is amplification of the DHFR gene. DHFR amplification leads to overexpression of MSH3 and has been tied drug-resistant recurrence in cancer.

In contrast, loss of MSH3 can lead to mismatch repair deficiency and genetic instability which have been identified as particularly common carcinogenic effects in human colorectal cancer. Mutations causing MSH3 knockdown can lead to diminished capacity for cells to repair long insertion/deletion loops causing microsatellite instabilities (MSI) in the genome and allowing an increase in the rates of somatic mutation. Elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) are a type of MSI where loci containing AAAG or ATAG tetranucleotide repeats are particularly unstable. EMAST phenotypes are particularly common, with nearly 60% of sporadic colorectal cancers displaying high levels of EMAST linked to a high-rate of MSH3 deficient cells in tumors.

Further reading

• Marti TM, Kunz C, Fleck O (2002). "DNA mismatch repair and mutation avoidance pathways". J. Cell. Physiol. 191 (1): 28–41. doi:10.1002/jcp.10077. PMID 11920679. S2CID 35468455.
• Fujii H, Shimada T (1989). "Isolation and characterization of cDNA clones derived from the divergently transcribed gene in the region upstream from the human dihydrofolate reductase gene". J. Biol. Chem. 264 (17): 10057–64. doi:10.1016/S0021-9258(18)81766-5. PMID 2722860.
• Chen MJ, Shimada T, Moulton AD, et al. (1984). "The functional human dihydrofolate reductase gene". J. Biol. Chem. 259 (6): 3933–43. doi:10.1016/S0021-9258(17)43186-3. PMID 6323448.
• Shinya E, Shimada T (1994). "Identification of two initiator elements in the bidirectional promoter of the human dihydrofolate reductase and mismatch repair protein 1 genes". Nucleic Acids Res. 22 (11): 2143–9. doi:10.1093/nar/22.11.2143. PMC 308133. PMID 8029024.
• Risinger JI, Umar A, Boyd J, et al. (1996). "Mutation of MSH3 in endometrial cancer and evidence for its functional role in heteroduplex repair". Nat. Genet. 14 (1): 102–5. doi:10.1038/ng0996-102. PMID 8782829. S2CID 25456490.
• Watanabe A, Ikejima M, Suzuki N, Shimada T (1997). "Genomic organization and expression of the human MSH3 gene". Genomics. 31 (3): 311–8. doi:10.1006/geno.1996.0053. PMID 8838312.
• Nakajima E, Orimo H, Ikejima M, Shimada T (1996). "Nine-bp repeat polymorphism in exon 1 of the hMSH3 gene". Jpn. J. Hum. Genet. 40 (4): 343–5. doi:10.1007/BF01900603. PMID 8851770.
• Acharya S, Wilson T, Gradia S, et al. (1997). "hMSH2 forms specific mispair-binding complexes with hMSH3 and hMSH6". Proc. Natl. Acad. Sci. U.S.A. 93 (24): 13629–34. doi:10.1073/pnas.93.24.13629. PMC 19374. PMID 8942985.
• Guerrette S, Wilson T, Gradia S, Fishel R (1998). "Interactions of human hMSH2 with hMSH3 and hMSH2 with hMSH6: examination of mutations found in hereditary nonpolyposis colorectal cancer". Mol. Cell. Biol. 18 (11): 6616–23. doi:10.1128/mcb.18.11.6616. PMC 109246. PMID 9774676.
• Ceccotti S, Ciotta C, Fronza G, et al. (2000). "Multiple mutations and frameshifts are the hallmark of defective hPMS2 in pZ189-transfected human tumor cells". Nucleic Acids Res. 28 (13): 2577–84. doi:10.1093/nar/28.13.2577. PMC 102707. PMID 10871409.
• Orimo H, Nakajima E, Yamamoto M, et al. (2000). "Association between single nucleotide polymorphisms in the hMSH3 gene and sporadic colon cancer with microsatellite instability". J. Hum. Genet. 45 (4): 228–30. doi:10.1007/s100380070031. PMID 10944853.
• Clark AB, Valle F, Drotschmann K, et al. (2001). "Functional interaction of proliferating cell nuclear antigen with MSH2-MSH6 and MSH2-MSH3 complexes". J. Biol. Chem. 275 (47): 36498–501. doi:10.1074/jbc.C000513200. PMID 11005803.
• Kleczkowska HE, Marra G, Lettieri T, Jiricny J (2001). "hMSH3 and hMSH6 interact with PCNA and colocalize with it to replication foci". Genes Dev. 15 (6): 724–36. doi:10.1101/gad.191201. PMC 312660. PMID 11274057.
• Schmutte C, Sadoff MM, Shim KS, et al. (2001). "The interaction of DNA mismatch repair proteins with human exonuclease I." J. Biol. Chem. 276 (35): 33011–8. doi:10.1074/jbc.M102670200. PMID 11427529.
• Wang Q, Zhang H, Guerrette S, et al. (2001). "Adenosine nucleotide modulates the physical interaction between hMSH2 and BRCA1". Oncogene. 20 (34): 4640–9. doi:10.1038/sj.onc.1204625. PMID 11498787.
• Mazurek A, Berardini M, Fishel R (2002). "Activation of human MutS homologs by 8-oxo-guanine DNA damage". J. Biol. Chem. 277 (10): 8260–6. doi:10.1074/jbc.M111269200. PMID 11756455.
• Plotz G, Raedle J, Brieger A, et al. (2002). "hMutSalpha forms an ATP-dependent complex with hMutLalpha and hMutLbeta on DNA". Nucleic Acids Res. 30 (3): 711–8. doi:10.1093/nar/30.3.711. PMC 100294. PMID 11809883.
• Arzimanoglou II, Hansen LL, Chong D, et al. (2002). "Frequent LOH at hMLH1, a highly variable SNP in hMSH3, and negligible coding instability in ovarian cancer". Anticancer Res. 22 (2A): 969–75. PMID 12014680.
• Ohta S, Shiomi Y, Sugimoto K, et al. (2002). "A proteomics approach to identify proliferating cell nuclear antigen (PCNA)-binding proteins in human cell lysates. Identification of the human CHL12/RFCs2-5 complex as a novel PCNA-binding protein". J. Biol. Chem. 277 (43): 40362–7. doi:10.1074/jbc.M206194200. PMID 12171929.