title: Functional studies and homology modeling of Msh2-Msh3 predict that mispair recognition involves DNA bending and strand separation.
abstract: The Msh2-Msh3 heterodimer recognizes various DNA mispairs, including loops of DNA ranging from 1 to 14 nucleotides and some base-base mispairs. Homology modeling of the mispair-binding domain (MBD) of Msh3 using the related Msh6 MBD revealed that mismatch recognition must be different, even though the MBD folds must be similar. Model-based point mutation alleles of Saccharomyces cerevisiae msh3 designed to disrupt mispair recognition fell into two classes. One class caused defects in repair of both small and large insertion/deletion mispairs, whereas the second class caused defects only in the repair of small insertion/deletion mispairs; mutations of the first class also caused defects in the removal of nonhomologous tails present at the ends of double-strand breaks (DSBs) during DSB repair, whereas mutations of the second class did not cause defects in the removal of nonhomologous tails during DSB repair. Thus, recognition of small insertion/deletion mispairs by Msh3 appears to require a greater degree of interactions with the DNA conformations induced by small insertion/deletion mispairs than with those induced by large insertion/deletions that are intrinsically bent and strand separated. Mapping of the two classes of mutations onto the Msh3 MBD model appears to distinguish mispair recognition regions from DNA stabilization regions.
authors.affiliation: Ludwig Institute for Cancer Research, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA.
authors.forename: Jill M
authors.initials: JM
authors.lastname: Dowen
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Putnam
authors.forename: Richard D
authors.initials: RD
authors.lastname: Kolodner
mesh_terms: D000595:Amino Acid Sequence; D020137:Base Pair Mismatch; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004260:DNA Repair; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D051718:MutS Homolog 2 Protein / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D000074081:MutS Homolog 3 Protein; D016297:Mutagenesis, Site-Directed; D009690:Nucleic Acid Conformation; D017354:Point Mutation; D017434:Protein Structure, Tertiary; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D016415:Sequence Alignment
chemical_list: D004268:DNA-Binding Proteins; C081696:MSH3 protein, S cerevisiae; D000074081:MutS Homolog 3 Protein; D029701:Saccharomyces cerevisiae Proteins; D004247:DNA; C489751:MSH2 protein, S cerevisiae; D051718:MutS Homolog 2 Protein