The PMS2 Subunit of Human MutLα Contains a Metal Ion Binding Domain of the Iron-Dependent Repressor Protein Family

Kosiński, Jan; Plotz, Guido; Guarné, Alba; Bujnicki, Janusz M.; Friedhoff, Peter

doi:10.1016/j.jmb.2008.06.056

Cited by 56 publications

(98 citation statements)

References 97 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Crystallographic analyses on the C-terminal domain (CTD) of eukaryotic and bacterial MutL endonuclease have shown that the domain is composed of regulatory and dimerization subdomains (11, 26 -28). The dimerization subdomain contains the metal-binding site essential for the endonuclease activity (29), in which two zinc ions are coordinated by the residues from highly conserved motifs: DQHAX 2 EX 4 E, ACR, and CPHGRP (11,15,26,30). These motifs are conserved in MutL from the majority of organisms except for limited species in ␥-proteobacteria (12, 15, 16, 19 -21, 31).…”

Section: Dna Mismatch Repair (Mmr)mentioning

confidence: 99%

Structural Features and Functional Dependency on β-Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease MutL

Fukui

Baba

Kumasaka

et al. 2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

In early reactions of DNA mismatch repair, MutS recognizes mismatched bases and activates MutL endonuclease to incise the error-containing strand of the duplex. DNA sliding clamp is responsible for directing the MutL-dependent nicking to the newly synthesized/error-containing strand. In Bacillus subtilis MutL, the ␤-clamp-interacting motif (␤ motif) of the C-terminal domain (CTD) is essential for both in vitro direct interaction with ␤-clamp and in vivo repair activity. A large cluster of negatively charged residues on the B. subtilis MutL CTD prevents nonspecific DNA binding until ␤ clamp interaction neutralizes the negative charge. We found that there are some bacterial phyla whose MutL endonucleases lack the ␤ motif. For example, the region corresponding to the ␤ motif is completely missing in Aquifex aeolicus MutL, and critical amino acid residues in the ␤ motif are not conserved in Thermus thermophilus MutL. We then revealed the 1.35 Å-resolution crystal structure of A. aeolicus MutL CTD, which lacks the ␤ motif but retains the metalbinding site for the endonuclease activity. Importantly, there was no negatively charged cluster on its surface. It was confirmed that CTDs of ␤ motif-lacking MutLs, A. aeolicus MutL and T. thermophilus MutL, efficiently incise DNA even in the absence of ␤-clamp and that ␤-clamp shows no detectable enhancing effect on their activity. In contrast, CTD of Streptococcus mutans, a ␤ motif-containing MutL, required ␤-clamp for the digestion of DNA. We propose that MutL endonucleases are divided into three subfamilies on the basis of their structural features and dependence on ␤-clamp.

show abstract

Section: Dna Mismatch Repair (Mmr)mentioning

confidence: 99%

Structural Features and Functional Dependency on β-Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease MutL

Fukui

Baba

Kumasaka

et al. 2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…Function-structure evaluations were conducted with a model of human MLH1-PMS2 based on the structure of human PMS2-NTD (27) and homology models of MLH1-NTD and MLH1-PMS2-CTD (24,25,28). Figures were generated using PyMOL v.1.4.1 (Schr€ odinger LLC).…”

Section: Structural and Bioinformatic Analysesmentioning

confidence: 99%

Expression Defect Size among Unclassified MLH1 Variants Determines Pathogenicity in Lynch Syndrome Diagnosis

Hinrichsen

Brieger

Zeuzem

et al. 2013

Clinical Cancer Research

Self Cite

View full text Add to dashboard Cite

Purpose: Lynch syndrome is caused by a germline mutation in a mismatch repair gene, most commonly the MLH1 gene. However, one third of the identified alterations are missense variants with unclear clinical significance. The functionality of these variants can be tested in the laboratory, but the results cannot be used for clinical diagnosis. We therefore aimed to establish a laboratory test that can be applied clinically.Experimental Design: We assessed the expression, stability, and mismatch repair activity of 38 MLH1 missense variants and determined the pathogenicity status of recurrent variants using clinical data.Results: Four recurrent variants were classified as neutral (K618A, H718Y, E578G, V716M) and three as pathogenic (A681T, L622H, P654L). All seven variants were proficient in mismatch repair but showed defects in expression. Quantitative PCR, pulse-chase, and thermal stability experiments confirmed decreases in protein stability, which were stronger in the pathogenic variants. The minimal cellular MLH1 concentration for mismatch repair was determined, which corroborated that strongly destabilized variants can cause repair deficiency. Loss of MLH1 tumor immunostaining is consistently reported in carriers of the pathogenic variants, showing the impact of this protein instability on these tumors.Conclusions: Expression defects are frequent among MLH1 missense variants, but only severe defects cause Lynch syndrome. The data obtained here enabled us to establish a threshold for distinguishing tolerable (clinically neutral) from pathogenic expression defects. This threshold allows the translation of laboratory results for uncertain MLH1 variants into pathogenicity statements for diagnosis, thereby improving the targeting of cancer prevention measures in affected families.

show abstract

“…The majority of bacteria possess MutS and MutL dimers whose fundamental characteristics are similar to those of human MutS␣ and MutL␣, respectively. Bacterial MutL homologs show high amino acid sequence similarity to the PMS2 subunit of human MutL␣, which includes the endonuclease motif, DQHAX 2 EX 4 E, and the zinc-binding motif, CPHGRP, in the C-terminal domain (CTD) (6,9,10). To date, it has been confirmed that MutL proteins from Thermus thermophilus, Aquifex aeolicus, Neisseria gonorrhoeae, and Bacillus subtilis possess nicking endonuclease activity (9,(11)(12)(13).…”

mentioning

confidence: 98%

Evidence for ATP-dependent Structural Rearrangement of Nuclease Catalytic Site in DNA Mismatch Repair Endonuclease MutL

Yamamoto

Iino

Kuramitsu

et al. 2011

Journal of Biological Chemistry

View full text Add to dashboard Cite

DNA mismatch repair (MMR) greatly contributes to genome integrity via the correction of mismatched bases that are mainly generated by replication errors. Postreplicative MMR excises a relatively long tract of error-containing single-stranded DNA. MutL is a widely conserved nicking endonuclease that directs the excision reaction to the error-containing strand of the duplex by specifically nicking the daughter strand. Because MutL apparently exhibits nonspecific nicking endonuclease activity in vitro, the regulatory mechanism of MutL has been argued. Recent studies suggest ATP-dependent conformational and functional changes of MutL, indicating that the regulatory mechanism involves the ATP binding and hydrolysis cycle. In this study, we investigated the effect of ATP binding on the structure of MutL. First, a cross-linking experiment confirmed that the N-terminal ATPase domain physically interacts with the C-terminal endonuclease domain. Next, hydrogen/deuterium exchange mass spectrometry clarified that the binding of ATP to the N-terminal domain induces local structural changes at the catalytic sites of MutL C-terminal domain. Finally, on the basis of the results of the hydrogen/deuterium exchange experiment, we successfully identified novel regions essential for the endonuclease activity of MutL. The results clearly show that ATP modulates the nicking endonuclease activity of MutL via structural rearrangements of the catalytic site. In addition, several Lynch syndrome-related mutations in human MutL homolog are located in the position corresponding to the newly identified catalytic region. Our data contribute toward understanding the relationship between mutations in MutL homolog and human disease.The DNA mismatch repair (MMR) 4 system greatly contributes to the replication fidelity of DNA by correcting the mismatched bases generated by the errors of DNA polymerases (1-3). The early reactions of eukaryotic MMR are performed mainly by MutS␣ (MSH2/MSH6 heterodimer) and MutL␣ (PMS2/MLH1 and PMS1/MLH1 heterodimers in Homo sapiens and Saccharomyces cerevisiae, respectively). It is reported that hereditary dysfunctions of these proteins are a major cause of Lynch syndrome (also known as hereditary non-polyposis colorectal cancer) in humans (4,5). MutS␣ recognizes the mismatched bases and stimulates MutL␣, which has a latent nicking endonuclease activity that introduces the entry or termination point of the subsequent excision reaction (6 -8). MutL␣ directs MMR to the daughter strand by specifically nicking the discontinuous strand in cooperation with replication protein A as well as the loaded form of proliferating cell nuclear antigen in the presence of ATP (7). After the error-containing strand is excised by EXO1, DNA polymerase ␦ resynthesizes the strand to complete the repair reaction.The MMR systems of the majority of bacteria except Escherichia coli and other ␥-proteobacteria are believed to resemble the eukaryotic system (8). The majority of bacteria possess MutS and MutL dimers whose fundamental characterist...

show abstract

The PMS2 Subunit of Human MutLα Contains a Metal Ion Binding Domain of the Iron-Dependent Repressor Protein Family

Cited by 56 publications

References 97 publications

Structural Features and Functional Dependency on β-Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease MutL

Structural Features and Functional Dependency on β-Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease MutL

Expression Defect Size among Unclassified MLH1 Variants Determines Pathogenicity in Lynch Syndrome Diagnosis

Evidence for ATP-dependent Structural Rearrangement of Nuclease Catalytic Site in DNA Mismatch Repair Endonuclease MutL

Contact Info

Product

Resources

About