title: Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS.
abstract: The haloacid dehalogenase (HAD)-like enzymes comprise a large superfamily of phosphohydrolases present in all organisms. The Saccharomyces cerevisiae genome encodes at least 19 soluble HADs, including 10 uncharacterized proteins. Here, we biochemically characterized 13 yeast phosphatases from the HAD superfamily, which includes both specific and promiscuous enzymes active against various phosphorylated metabolites and peptides with several HADs implicated in detoxification of phosphorylated compounds and pseudouridine. The crystal structures of four yeast HADs provided insight into their active sites, whereas the structure of the YKR070W dimer in complex with substrate revealed a composite substrate-binding site. Although the S. cerevisiae and Escherichia coli HADs share low sequence similarities, the comparison of their substrate profiles revealed seven phosphatases with common preferred substrates. The cluster of secondary substrates supporting significant activity of both S. cerevisiae and E. coli HADs includes 28 common metabolites that appear to represent the pool of potential activities for the evolution of novel HAD phosphatases. Evolution of novel substrate specificities of HAD phosphatases shows no strict correlation with sequence divergence. Thus, evolution of the HAD superfamily combines the conservation of the overall substrate pool and the substrate profiles of some enzymes with remarkable biochemical and structural flexibility of other superfamily members.
authors.affiliation: From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Kuznetsova
authors.affiliation: the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439.
authors.forename: Boguslaw
authors.initials: B
authors.lastname: Nocek
authors.affiliation: the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada.
authors.forename: Greg
authors.initials: G
authors.lastname: Brown
authors.affiliation: the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894.
authors.forename: Kira S
authors.initials: KS
authors.lastname: Makarova
authors.affiliation: the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada.
authors.forename: Robert
authors.initials: R
authors.lastname: Flick
authors.affiliation: the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894.
authors.forename: Yuri I
authors.initials: YI
authors.lastname: Wolf
authors.affiliation: the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada.
authors.forename: Anna
authors.initials: A
authors.lastname: Khusnutdinova
authors.affiliation: the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada.
authors.forename: Elena
authors.initials: E
authors.lastname: Evdokimova
authors.affiliation: the Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada, and.
authors.forename: Ke
authors.initials: K
authors.lastname: Jin
authors.affiliation: the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439.
authors.forename: Kemin
authors.initials: K
authors.lastname: Tan
authors.affiliation: the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Hanson
authors.affiliation: the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611.
authors.forename: Ghulam
authors.initials: G
authors.lastname: Hasnain
authors.affiliation: the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611.
authors.forename: Rémi
authors.initials: R
authors.lastname: Zallot
authors.affiliation: the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611.
authors.forename: Valérie
authors.initials: V
authors.lastname: de Crécy-Lagard
authors.affiliation: the Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada, and.
authors.forename: Mohan
authors.initials: M
authors.lastname: Babu
authors.affiliation: the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada.
authors.forename: Alexei
authors.initials: A
authors.lastname: Savchenko
authors.affiliation: the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Joachimiak
authors.affiliation: From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439.
authors.forename: Aled M
authors.initials: AM
authors.lastname: Edwards
authors.affiliation: the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894.
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
authors.affiliation: the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada, a.iakounine@utoronto.ca.
authors.forename: Alexander F
authors.initials: AF
authors.lastname: Yakunin
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D001665:Binding Sites; D002384:Catalysis; D020134:Catalytic Domain / Q000235:genetics; D018360:Crystallography, X-Ray; D019143:Evolution, Molecular; D016681:Genome, Fungal; D006867:Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D007700:Kinetics; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D012441:Saccharomyces cerevisiae / Q000201:enzymology*; D016415:Sequence Alignment; D013379:Substrate Specificity
chemical_list: D006867:Hydrolases; C034507:2-haloacid dehalogenase
keywords: Saccharomyces cerevisiae; crystal structure; enzyme catalysis; haloacid dehalogenase; phosphatase; substrate specificity