title: Crystal structure of YdaL, a stand-alone small MutS-related protein from Escherichia coli.
abstract: 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.
authors.affiliation: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China.
authors.forename: Wen-Jun
authors.initials: WJ
authors.lastname: Gui
authors.forename: Qian-Hui
authors.initials: QH
authors.lastname: Qu
authors.forename: Yuan-Yuan
authors.initials: YY
authors.lastname: Chen
authors.forename: Ming
authors.initials: M
authors.lastname: Wang
authors.forename: Xian-En
authors.initials: XE
authors.lastname: Zhang
authors.forename: Li-Jun
authors.initials: LJ
authors.lastname: Bi
authors.forename: Tao
authors.initials: T
authors.lastname: Jiang
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D004720:Endonucleases / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D051719:MutS DNA Mismatch-Binding Protein / Q000737:chemistry; D010446:Peptide Fragments / Q000737:chemistry*; D011119:Polynucleotides / Q000378:metabolism; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D040681:Structural Homology, Protein
chemical_list: D029968:Escherichia coli Proteins; D010446:Peptide Fragments; D011119:Polynucleotides; D004720:Endonucleases; C560187:YdaL protein, E coli; D051719:MutS DNA Mismatch-Binding Protein; C497175:MutS protein, E coli