부산대학교 도서관

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.jmb.2008.09.005 Byline: Tammo Diercks, Eiso AB, Mark A. Daniels, Rob N. de Jong, Rogier Besseling, Robert Kaptein, Gert E. Folkers Keywords: DNA repair; IF3C fold; NMR; DNA-binding domain; DNase I Abbreviations: Smr, small MutS-related; dsDNA, double-stranded DNA; ssDNA, single-stranded DNA; B3BP, Bcl3-binding protein; N4BP2, Nedd4-binding protein 2; EMSA, electrophoretic mobility shift assay; GST, glutathione S-transferase; EDTA, ethylenediaminetetraacetic acid; HSQC, heteronuclear single quantum coherence; NOE, nuclear Overhauser enhancement 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. Author Affiliation: Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Faculty of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands Article History: Received 25 July 2008; Revised 1 September 2008; Accepted 3 September 2008 Article Note: (miscellaneous) Edited by M. F. Summers