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PDBsum entry 1rlo
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References listed in PDB file
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Key reference
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Title
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Ybiv from escherichia coli k12 is a had phosphatase.
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Authors
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A.Roberts,
S.Y.Lee,
E.Mccullagh,
R.E.Silversmith,
D.E.Wemmer.
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Ref.
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Proteins, 2005,
58,
790-801.
[DOI no: ]
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PubMed id
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Abstract
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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.
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Figure 1.
Figure 1. A: Ribbon diagram of the structure of YbiV. The
hydrolase domain is colored in medium grey, the inserted domain
in light grey. The nucleophilic aspartate and the magnesium ion
are dark grey. B: Secondary structure topology of YbiV shaded
similarly to A. C: Overlay of the hydrolase domains of PSP
(pink) and YrbI (blue) onto the full structure of YbiV (grey),
all as alpha carbon backbones. The full structures of the PSP
and YrbI monomers (top and bottom, respectively) are shown to
the right as ribbons. D: Surface potential plot of YbiV. Acidic
regions are shown in red, basic regions in blue. (Fig.
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Figure 3.
Figure 3. A: Stereoview of the native active-site of YbiV. The
magnesium ion is represented by a magenta sphere, water
molecules as blue spheres. Hydrogen bonds are represented as
dashed lines and numbers indicate distances in Angstroms. The
active-site motifs are labeled. B: Overlay of the active-sites
of YrbI from H. influenzae (green) and YbiV (blue.) The blue
sphere represents magnesium, the green sphere, cobalt. The
residue numbers are labeled, YbiV on the left, YrbI on the right.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2005,
58,
790-801)
copyright 2005.
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