YbiV from E. coli K12 is a HAD phosphatase

Journal Article · Tue Mar 16 04:00:00 EST 2004 · Proteins: Structure, Function, Bioinformatics

OSTI ID:840329

Roberts, Anne ^[1]; Lee, Seok-Yong; McCullagh, Emma; Silversmith, Ruth E; Wemmer, David E

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1. LBNL Library

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 a/b 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 which 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.

• Research Organization: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)
• Sponsoring Organization: USDOE Director, Office of Science; National Institutes of Health (US)
• DOE Contract Number: AC03-76SF00098
• OSTI ID: 840329
• Report Number(s): LBNL--54737
• Journal Information: Proteins: Structure, Function, Bioinformatics, Journal Name: Proteins: Structure, Function, Bioinformatics Journal Issue: 4 Vol. 58
• Country of Publication: United States
• Language: English

Related Subjects

36 MATERIALS SCIENCE
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
ALUMINIUM
CRYSTAL STRUCTURE
ESCHERICHIA COLI
FUNCTIONALS
HYDROLASES
HYDROLYSIS
PHOSPHATASE YBIV PHOSPHOASPARTATE INTERMEDIATE HAD SUPERFAMILY
PHOSPHATASES
PHOSPHATES
PROTEINS
SACCHAROSE
STRUCTURAL CHEMICAL ANALYSIS
SUBSTRATES