Sequence homologs of the small MutS-related (Smr) domain, the C-terminal endonuclease domain of MutS2, also exist as stand-alone proteins. In this study, we report the crystal structure of a proteolyzed fragment of YdaL(YdaL(39-175)). a stand-alone Smr protein from Escherichia colt In this structure, residues 86-170 assemble into a classical Smr core domain and are embraced by an N-terminal extension (residues 40-85) with an alpha/beta/ a fold. Sequence alignment indicates that the N-terminal extension is conserved among a number of stand-alone Smr proteins, suggesting structural diversity among Smr domains. We also discovered that the DNA binding affinity and endonuclease activity of the truncated YdaL(39-175) protein were slightly lower than those of full-length YdaL(1-187), suggesting that residues 1-38 may be involved in DNA binding. (C) 2011 Elsevier Inc. All rights reserved.