title: Solution structure and characterization of the DNA-binding activity of the B3BP-Smr domain.
abstract: The MutS1 protein recognizes unpaired bases and initiates mismatch repair, which are essential for high-fidelity DNA replication. The homologous MutS2 protein does not contribute to mismatch repair, but suppresses homologous recombination. MutS2 lacks the damage-recognition domain of MutS1, but contains an additional C-terminal extension: the small MutS-related (Smr) domain. This domain, which is present in both prokaryotes and eukaryotes, has previously been reported to bind to DNA and to possess nicking endonuclease activity. We determine here the solution structure of the functionally active Smr domain of the Bcl3-binding protein (also known as Nedd4-binding protein 2), a protein with unknown function that lacks other domains present in MutS proteins. The Smr domain adopts a two-layer alpha-beta sandwich fold, which has a structural similarity to the C-terminal domain of IF3, the R3H domain, and the N-terminal domain of DNase I. The most conserved residues are located in three loops that form a contiguous, exposed, and positively charged surface with distinct sequence identity for prokaryotic and eukaryotic Smr domains. NMR titration experiments and DNA binding studies using Bcl3-binding protein-Smr domain mutants suggested that these most conserved loop regions participate in DNA binding to single-stranded/double-stranded DNA junctions. Based on the observed DNA-binding-induced multimerization, the structural similarity with both subdomains of DNase I, and the experimentally identified DNA-binding surface, we propose a model for DNA recognition by the Smr domain.
authors.affiliation: Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Faculty of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors.forename: Tammo
authors.initials: T
authors.lastname: Diercks
authors.forename: Eiso
authors.initials: E
authors.lastname: AB
authors.forename: Mark A
authors.initials: MA
authors.lastname: Daniels
authors.forename: Rob N
authors.initials: RN
authors.lastname: de Jong
authors.forename: Rogier
authors.initials: R
authors.lastname: Besseling
authors.forename: Robert
authors.initials: R
authors.lastname: Kaptein
authors.forename: Gert E
authors.initials: GE
authors.lastname: Folkers
mesh_terms: D000595:Amino Acid Sequence; D002352:Carrier Proteins / Q000737:chemistry* / Q000378:metabolism*; D002460:Cell Line; D017124:Conserved Sequence; D004247:DNA / Q000378:metabolism*; D045643:DNA Repair Enzymes; D004720:Endonucleases / Q000378:metabolism; D005057:Eukaryotic Cells / Q000737:chemistry; D019143:Evolution, Molecular; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011387:Prokaryotic Cells / Q000737:chemistry; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D012996:Solutions; D040681:Structural Homology, Protein
chemical_list: D002352:Carrier Proteins; C476254:N4BP2 protein, human; D012996:Solutions; D004247:DNA; D004720:Endonucleases; D045643:DNA Repair Enzymes