The Phe-X-Glu DNA Binding Motif of MutS

Schofield, Mark; Brownewell, Floyd E.; Nayak, Sunil; Du, Chunwei; Kool, Eric T.; Hsieh, Peggy

doi:10.1074/jbc.c100449200

Cited by 87 publications

(58 citation statements)

References 26 publications

(23 reference statements)

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“…Indeed, the affinities and specificities of MutS-E41A for these sites differ only slightly from those of wtMutS (Table 1). These results are consistent with biochemical studies, which show no significant differences between T. aquaticus wtMutS and MutS-E41A affinities or specificities for GT mismatch or T-bulge containing DNA (21); however, the corresponding mutant from E. coli exhibited a modest increase in nonspecific binding and a decrease in specificity (21,22).…”

Section: Resultssupporting

confidence: 91%

“…Glu 41 -dependent Formation of the Unbent URC Is Necessary to Signal Repair-In contrast to mutation of the conserved Phe residue, mutation of the conserved Glu to Ala in T. aquaticus MutS (E41A) or E. coli MutS (E38A) has little effect on the binding affinities and specificities for a GT mismatch or a T-bulge (Table 1) (21,22). In addition, the crystal structures of wild type and E38A E. coli MutS are very similar to one another (22).…”

Section: Phe 39 Does Not Induce Dna Bending But Rather It Induces Thementioning

confidence: 99%

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Mechanism of MutS Searching for DNA Mismatches and Signaling Repair

Teßmer

Yang

Zhai

et al. 2008

Journal of Biological Chemistry

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112

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Section: Resultssupporting

confidence: 91%

Section: Phe 39 Does Not Induce Dna Bending But Rather It Induces Thementioning

confidence: 99%

Mechanism of MutS Searching for DNA Mismatches and Signaling Repair

Teßmer

Yang

Zhai

et al. 2008

Journal of Biological Chemistry

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112

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“…Consistent with our results, a recent study (14) indicates that the glutamate in MutS homologous to Msh6 Glu 339 contributes to MMR and mismatched DNA binding specificity via a hydrogen bond and charge repulsion. A comparison of the two studies also reveals three differences that deserve further investigation.…”

Section: Biochemical Analysis Of Mutant Proteins With Changes In Resisupporting

confidence: 93%

“…Finally, we use both amino acid replacement and DNA substrate modification to test the hypothesis that the side chain of Glu 339 in Msh6 forms a hydrogen bond with the mismatched base. Comparison with a recent study of MutS reveals common features and distinct differences between the bacterial and eukaryotic proteins when this glutamate is replaced with alanine (14).…”

mentioning

confidence: 78%

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Asymmetric Recognition of DNA Local Distortion

Drotschmann¹,

Yang²,

Brownewell³

et al. 2001

Journal of Biological Chemistry

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Crystal structures of bacterial MutS homodimers bound to mismatched DNA reveal asymmetric interactions of the two subunits with DNA. A phenylalanine and glutamate of one subunit make mismatched base-specific interactions, and residues of both subunits contact the DNA backbone surrounding the mismatched base, but asymmetrically. A number of amino acids in MutS that contact the DNA are conserved in the eukaryotic Msh2-Msh6 heterodimer. We report here that yeast strains with amino acids substituted for residues inferred to interact with the DNA backbone or mismatched base have elevated spontaneous mutation rates consistent with defective mismatch repair. Purified Msh2-Msh6 with substitutions in the conserved Phe 337 and Glu 339 in Msh6 thought to stack or hydrogen bond, respectively, with the mismatched base do have reduced DNA binding affinity but normal ATPase activity. Moreover, wild-type Msh2-Msh6 binds with lower affinity to mismatches with thymine replaced by difluorotoluene, which lacks the ability to hydrogen bond. The results suggest that yeast Msh2-Msh6 interacts asymmetrically with the DNA through base-specific stacking and hydrogen bonding interactions and backbone contacts. The importance of these contacts decreases with increasing distance from the mismatch, implying that interactions at and near the mismatch are important for binding in a kinked DNA conformation. DNA mismatch repair (MMR)1 in bacteria is initiated when MutS protein binds to mismatches in DNA. Details of this binding were revealed by the x-ray crystal structures of Thermus aquaticus (Taq) and Escherichia coli MutS homodimers bound to mismatched DNA (1, 2). Subunits A and B of the MutS homodimer are comprised of five domains, and interactions with DNA involve several amino acids in domain I of subunit A and a smaller number of amino acids in domain IV of subunit B (Fig. 1A). These include sequence-independent van der Waals and hydrogen bonding interactions with the DNA backbone. Also seen is stacking between a mismatched thymine and a phenylalanine known to be essential for DNA binding and MMR in E. coli (3-9). The structures further indicate a hydrogen bond between the N3 of the mismatched thymine and the O⑀2 of a specific glutamate. Although the Phe and Glu residues are present in both subunits of the homodimer, only the residues in subunit A interact with the mismatched base. Thus, mismatch recognition by bacterial MutS involves interactions with DNA that are asymmetrical in the two subunits.MMR in eukaryotes is initiated by homologs of MutS. Msh2 and Msh6 form a heterodimer that binds to DNA containing base-base and insertion/deletion mismatches (10 -13). Although structural information on Msh2-Msh6 is not available, two lines of evidence suggest that Msh2-Msh6 also binds to DNA in an asymmetric manner. First, substituting alanine for the phenylalanine in Msh6 (F337A in yMsh6, F432A in hMSH6) that is homologous to the bacterial residue reduces DNA binding and mismatch repair (8,9). In contrast, substituting alanine for a tyrosine i...

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The GIY‐YIG endonuclease domain of Arabidopsis MutS homolog 1 specifically binds to branched DNA structures

et al. 2018

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In plant organelle genomes, homeologous recombination between heteroallelic positions of repetitive sequences is increased by dysfunction of the gene encoding MutS homolog 1 (MSH1), a plant organelle‐specific homolog of bacterial mismatch‐binding protein MutS1. The C‐terminal region of plant MSH1 contains the GIY‐YIG endonuclease motif. The biochemical characteristics of plant MSH1 have not been investigated; accordingly, the molecular mechanism by which plant MSH1 suppresses homeologous recombination is unknown. Here, we characterized the recombinant GIY‐YIG domain of Arabidopsis thaliana MSH1, showing that the domain possesses branched DNA‐specific DNA‐binding activity. Interestingly, the domain exhibited no endonuclease activity, suggesting that the mismatch‐binding domain is required for DNA incision. Based on these results, we propose a possible mechanism for MSH1‐dependent suppression of homeologous recombination.

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The Phe-X-Glu DNA Binding Motif of MutS

Cited by 87 publications

References 26 publications

Mechanism of MutS Searching for DNA Mismatches and Signaling Repair

Mechanism of MutS Searching for DNA Mismatches and Signaling Repair

Asymmetric Recognition of DNA Local Distortion

The GIY‐YIG endonuclease domain of Arabidopsis MutS homolog 1 specifically binds to branched DNA structures

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