YbiV from Escherichia coli K12 is a HAD phosphatase.
The protein YbiV from Escherichia coli K12 MG1655 is a hypothetical protein with sequence homology to the haloacid dehalogenase (HAD) superfamily of proteins. Although numerous members of this family have been identified, the functions of few are known. Using the crystal structure, sequence analysis, and biochemical assays, we have characterized YbiV as a HAD phosphatase. The crystal structure of YbiV reveals a two-domain protein, one with the characteristic HAD hydrolase fold, the other an inserted alpha/beta fold. In an effort to understand the mechanism, we also solved and report the structures of YbiV in complex with beryllofluoride (BeF3-) and aluminum trifluoride (AlF3), which have been shown to mimic the phosphorylated intermediate and transition state for hydrolysis, respectively, in analogy to other HAD phosphatases. Analysis of the structures reveals the substrate-binding cavity, which is hydrophilic in nature. Both structure and sequence homology indicate YbiV may be a sugar phosphatase, which is supported by biochemical assays that measured the release of free phosphate on a number of sugar-like substrates. We also investigated available genomic and functional data in an effort to determine the physiological substrate.
Roberts
Anne
A
Department of Chemistry, University of California, Berkeley, California 94720, USA.
Lee
Seok-Yong
SY
McCullagh
Emma
E
Silversmith
Ruth E
RE
Wemmer
David E
DE
D000249:Adenosine Monophosphate / Q000737:chemistry; D017607:Aluminum Compounds / Q000737:chemistry; D000595:Amino Acid Sequence; D001608:Beryllium / Q000737:chemistry; D001665:Binding Sites; D002384:Catalysis; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins; D005459:Fluorides / Q000737:chemistry; D005461:Fluorine / Q000737:chemistry; D023281:Genomics / Q000379:methods; D006867:Hydrolases / Q000737:chemistry*; D006868:Hydrolysis; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D010749:Phosphoprotein Phosphatases / Q000737:chemistry* / Q000502:physiology; D010744:Phosphoric Monoester Hydrolases / Q000737:chemistry*; D010766:Phosphorylation; D011485:Protein Binding; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
D017607:Aluminum Compounds; D029968:Escherichia coli Proteins; D005461:Fluorine; D000249:Adenosine Monophosphate; C035982:beryllium fluoride; D006867:Hydrolases; D010749:Phosphoprotein Phosphatases; C510856:YbiV protein, E coli; D010744:Phosphoric Monoester Hydrolases; C034507:2-haloacid dehalogenase; D001608:Beryllium; D005459:Fluorides; C032311:aluminum fluoride