1RLO
Phospho-aspartyl Intermediate Analogue of ybiV from E. coli K12
Summary for 1RLO
Entry DOI | 10.2210/pdb1rlo/pdb |
Related | 1RLM 1RLT |
Descriptor | Phosphatase, MAGNESIUM ION, GLYCEROL, ... (4 entities in total) |
Functional Keywords | beryllium trifluoride, had family, phospho-aspartate, hydrolase |
Biological source | Escherichia coli |
Total number of polymer chains | 4 |
Total formula weight | 122576.92 |
Authors | Roberts, A.,Lee, S.Y.,McCullagh, E.,Silversmith, R.E.,Wemmer, D.E. (deposition date: 2003-11-26, release date: 2004-12-07, Last modification date: 2024-11-06) |
Primary citation | Roberts, A.,Lee, S.Y.,McCullagh, E.,Silversmith, R.E.,Wemmer, D.E. Ybiv from Escherichia coli K12 is a HAD phosphatase. Proteins, 58:790-801, 2005 Cited by PubMed Abstract: 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. PubMed: 15657928DOI: 10.1002/prot.20267 PDB entries with the same primary citation |
Experimental method | X-RAY DIFFRACTION (2 Å) |
Structure validation
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