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PDBsum entry 1w3u
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References listed in PDB file
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Key reference
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Title
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Enzyme adaptation to alkaline ph: atomic resolution (1.08 a) structure of phosphoserine aminotransferase from bacillus alcalophilus.
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Authors
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A.P.Dubnovitsky,
E.G.Kapetaniou,
A.C.Papageorgiou.
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Ref.
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Protein Sci, 2005,
14,
97.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of the vitamin B(6)-dependent enzyme phosphoserine
aminotransferase from the obligatory alkaliphile Bacillus alcalophilus has been
determined at 1.08 A resolution. The model was refined to an R-factor of 11.7%
(R(free) = 13.9%). The enzyme displays a narrow pH optimum of enzymatic activity
at pH 9.0. The final structure was compared to the previously reported structure
of the mesophilic phosphoserine aminotransferase from Escherichia coli and to
that of phosphoserine aminotransferase from a facultative alkaliphile, Bacillus
circulans subsp. alkalophilus. All three enzymes are homodimers with each
monomer comprising a two-domain architecture. Despite the high structural
similarity, the alkaliphilic representatives possess a set of distinctive
structural features. Two residues directly interacting with
pyridoxal-5'-phosphate are replaced, and an additional hydrogen bond to the O3'
atom of the cofactor is present in alkaliphilic phosphoserine aminotransferases.
The number of hydrogen bonds and hydrophobic interactions at the dimer interface
is increased. Hydrophobic interactions between the two domains in the monomers
are enhanced. Moreover, the number of negatively charged amino acid residues
increases on the solvent-accessible molecular surface and fewer hydrophobic
residues are exposed to the solvent. Further, the total amount of ion pairs and
ion networks is significantly reduced in the Bacillus enzymes, while the total
number of hydrogen bonds is increased. The mesophilic enzyme from Escherichia
coli contains two additional beta-strands in a surface loop with a third
beta-strand being shorter in the structure. The identified structural features
are proposed to be possible factors implicated in the alkaline adaptation of
phosphoserine aminotransferase.
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Figure 3.
Figure 3. Ribbon representation of the BALC PSAT dimer. The
two monomers are depicted in yellow and in blue, respectively.
Ligands included in the final model (PLP, PEG, HEPES, glycerol)
are shown in ball-and-sticks. Mg2+ ions are shown as gray
spheres and Cl- ions as pink spheres. (A) View along the twofold
noncrystallographic axis. The active site clefts are shown with
arrows. (B) BALC PSAT dimer after 90° rotation. The twofold axis
in this orientation is vertical and lying within the plane of
the figure. The figure was produced using MOLSCRIPT (Kraulis
1991) and Raster3D (Merritt and Murphy 1994).
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Figure 5.
Figure 5. Definition of torsion angle for the internal
aldimine bond and atom names in pyridoxal-5'-phosphate. The
figure was produced using ISIS/Draw (MDL, Inc.).
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The above figures are
reprinted
by permission from the Protein Society:
Protein Sci
(2005,
14,
97-0)
copyright 2005.
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