Crystal structure of YdaL, a stand-alone small MutS-related protein from Escherichia coli

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 (YdaL39–175), a stand-alone Smr protein from Escherichia coli. 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 α/β/α 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 YdaL39–175 protein were slightly lower than those of full-length YdaL1–187, suggesting that residues 1–38 may be involved in DNA binding.