title: Correlated Mutation in the Evolution of Catalysis in Uracil DNA Glycosylase Superfamily.
abstract: Enzymes in Uracil DNA glycosylase (UDG) superfamily are essential for the removal of uracil. Family 4 UDGa is a robust uracil DNA glycosylase that only acts on double-stranded and single-stranded uracil-containing DNA. Based on mutational, kinetic and modeling analyses, a catalytic mechanism involving leaving group stabilization by H155 in motif 2 and water coordination by N89 in motif 3 is proposed. Mutual Information analysis identifies a complexed correlated mutation network including a strong correlation in the EG doublet in motif 1 of family 4 UDGa and in the QD doublet in motif 1 of family 1 UNG. Conversion of EG doublet in family 4 Thermus thermophilus UDGa to QD doublet increases the catalytic efficiency by over one hundred-fold and seventeen-fold over the E41Q and G42D single mutation, respectively, rectifying the strong correlation in the doublet. Molecular dynamics simulations suggest that the correlated mutations in the doublet in motif 1 position the catalytic H155 in motif 2 to stabilize the leaving uracilate anion. The integrated approach has important implications in studying enzyme evolution and protein structure and function.
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Rooms 049 and 051 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA.
authors.forename: Bo
authors.initials: B
authors.lastname: Xia
authors.affiliation: Department of Chemistry, Clemson University, 367 Hunter Laboratories, Clemson, SC 29634, USA.
authors.forename: Yinling
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Rooms 049 and 051 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA.
authors.forename: Jose
authors.initials: J
authors.lastname: Guevara
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Rooms 049 and 051 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA.
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Rooms 049 and 051 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA.
authors.forename: Celeste
authors.initials: C
authors.lastname: Jilich
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Rooms 049 and 051 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA.
authors.forename: Ye
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Rooms 049 and 051 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA.
authors.forename: Liangjiang
authors.initials: L
authors.lastname: Wang
authors.affiliation: Department of Chemistry, Clemson University, 367 Hunter Laboratories, Clemson, SC 29634, USA.
authors.forename: Brian N
authors.initials: BN
authors.lastname: Dominy
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Rooms 049 and 051 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, USA.
authors.forename: Weiguo
authors.initials: W
authors.lastname: Cao
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D001665:Binding Sites; D055162:Biocatalysis; D005075:Biological Evolution; D007700:Kinetics; D008958:Models, Molecular; D005810:Multigene Family; D050505:Mutant Proteins / Q000737:chemistry / Q000378:metabolism; D009154:Mutation / Q000235:genetics*; D016415:Sequence Alignment; D013379:Substrate Specificity; D016963:Thermus thermophilus / Q000201:enzymology*; D014498:Uracil / Q000378:metabolism; D051981:Uracil-DNA Glycosidase / Q000737:chemistry / Q000235:genetics*
chemical_list: D050505:Mutant Proteins; D014498:Uracil; D051981:Uracil-DNA Glycosidase