Structures of Escherichia coli DNA mismatch repair enzyme MutS in complex with different mismatches: a common recognition mode for diverse substrates

Abstract

We have refined a series of isomorphous crystal structures of the Escherichia coli DNA mismatch repair enzyme MutS in complex with G:T, A:A, C:A and G:G mismatches and also with a single unpaired thymidine. In all these structures, the DNA is kinked by approximately 60 degrees upon protein binding. Two residues widely conserved in the MutS family are involved in mismatch recognition. The phenylalanine, Phe 36, is seen stacking on one of the mismatched bases. The same base is also seen forming a hydrogen bond to the glutamate Glu 38. This hydrogen bond involves the N7 if the base stacking on Phe 36 is a purine and the N3 if it is a pyrimidine (thymine). Thus, MutS uses a common binding mode to recognize a wide range of mismatches.

DNA mismatch repair: Molecular mechanism, cancer, and ageing

“…Co-crystal structures of MutS proteins containing short, C-terminal truncations from E. coli and T. aquaticus bound to a variety of mispairs and IDLs reveal a homodimeric protein clamped around the DNA at the mismatch (see Fig. 2; Junop et al, 2001;Lamers et al, 2000;Natrajan et al, 2003;Obmolova et al, 2000). The homodimers form a θ where the mismatched DNA resides in the lower channel while the upper channel is unoccupied.…”

Specialized mismatch repair function of Glu339 in the Phe-X-Glu motif of yeast Msh6

“…MutS is required to repair a wide variety of polymerization errors and can bind all possible single base-base mismatches and duplexes containing one to three extra bases in one strand [2,3]. Crystal structures of E. coli and Taq MutS bound to mismatched DNA [4][5][6][7] reveal that most contacts with the DNA are to the backbone. Only a phenylalanine and a glutamate in one monomer of MutS directly contact the mismatched base, and both are part of a Phe-X-Glu motif that is conserved in many bacterial and eukaryotic MutS proteins [4][5][6][7].…”

“…Crystal structures of E. coli and Taq MutS bound to mismatched DNA [4][5][6][7] reveal that most contacts with the DNA are to the backbone. Only a phenylalanine and a glutamate in one monomer of MutS directly contact the mismatched base, and both are part of a Phe-X-Glu motif that is conserved in many bacterial and eukaryotic MutS proteins [4][5][6][7]. The phenylalanine stacks with a mismatched or unpaired base and is essential for mismatch binding and for MMR function in E. coli and in eukaryotes [8][9][10][11].…”

“…The phenylalanine stacks with a mismatched or unpaired base and is essential for mismatch binding and for MMR function in E. coli and in eukaryotes [8][9][10][11]. The side chain of the glutamate also interacts with the mismatched base, including forming a hydrogen bond to purines or pyrimidines in base-base mismatches as well as in single-base insertion-deletion mismatches [4][5][6][7]. The conservation of this glutamate and the structural similarities in base specific contacts among E. coli and Taq MutS bound to several different single base mismatches [4][5][6][7], implies that this glutamate participates in repairing both single base substitution and single base insertion-deletion mismatches in these two bacteria.…”

“…The side chain of the glutamate also interacts with the mismatched base, including forming a hydrogen bond to purines or pyrimidines in base-base mismatches as well as in single-base insertion-deletion mismatches [4][5][6][7]. The conservation of this glutamate and the structural similarities in base specific contacts among E. coli and Taq MutS bound to several different single base mismatches [4][5][6][7], implies that this glutamate participates in repairing both single base substitution and single base insertion-deletion mismatches in these two bacteria. Previous studies have shown that replacement of Glu38 in E. coli MutS with other amino acids results in defective repair of base substitution mismatches [4,12,13].…”