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1RLO

Phospho-aspartyl Intermediate Analogue of ybiV from E. coli K12

Summary for 1RLO
Entry DOI10.2210/pdb1rlo/pdb
Related1RLM 1RLT
DescriptorPhosphatase, MAGNESIUM ION, GLYCEROL, ... (4 entities in total)
Functional Keywordsberyllium trifluoride, had family, phospho-aspartate, hydrolase
Biological sourceEscherichia coli
Total number of polymer chains4
Total formula weight122576.92
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 citationRoberts, 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: 15657928
DOI: 10.1002/prot.20267
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2 Å)
Structure validation

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