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PDBsum entry 2efx
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References listed in PDB file
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Key reference
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Title
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Structures of d-Amino-Acid amidase complexed with l-Phenylalanine and with l-Phenylalanine amide: insight into the d-Stereospecificity of d-Amino-Acid amidase from ochrobactrum anthropi sv3.
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Authors
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S.Okazaki,
A.Suzuki,
T.Mizushima,
H.Komeda,
Y.Asano,
T.Yamane.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2008,
64,
331-334.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structures of D-amino-acid amidase (DAA) from Ochrobactrum anthropi
SV3 in complex with L-phenylalanine and with L-phenylalanine amide were
determined at 2.3 and 2.2 A resolution, respectively. Comparison of the
L-phenylalanine amide complex with the D-phenylalanine complex reveals that the
D-stereospecificity of DAA might be achieved as a consequence of three
structural factors: (i) the hydrophobic cavity in the region in which the
hydrophobic side chain of the substrate is held, (ii) the spatial arrangement of
Gln310 O and Glu114 O epsilon2 that fixes the amino N atom of the substrate and
(iii) the existence of two cavities that keep the carboxyl/amide group of the
substrate near or apart from Ser60 O gamma.
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Figure 2.
Figure 2 (a) Active-site residues of molecule A (ordered type)
of the L-Phe-NH[2] complex. C atoms are shown in grey, O atoms
in red and N atoms in blue. A  [A]-weighted
F[o] - F[c] L-Phe-NH[2] OMIT map contoured at 3.0 is
superposed in grey. Broken red lines represent hydrogen bonds.
(b) Active-site residues of moleucle E (disordered type) of the
L-Phe-NH[2] complex. C atoms are shown in light green. [A]-Weighted
F[o] - F[c] L-Phe-NH[2] OMIT maps contoured at 3.0 and
2.0 are
superposed in grey and cyan, respectively. (c) Stereoview of the
superposition of the active-site residues of molecule E in the
L-Phe-NH[2] complex and those in the D-Phe complex. The
hypothetical mirror plane is shown as a black line. For the
L-Phe-NH[2] complex, C atoms are shown in light green and
hydrogen bonds are shown as red broken lines. For the D-Phe
complex, C atoms are shown in pink and hydrogen bonds are shown
as magenta broken lines. (d) Schematic representation of the
binding mode of L-Phe-NH[2] and D-Phe in molecule E of DAA.
L-Phe-NH[2] and D-Phe are shown in red. The hydrophobic cavity
for holding the side chain and the space for anchoring the amino
N atom are labelled (1) and (2), respectively. The cavities in
which the amide group of L-Phe-NH[2] and the carboxyl group of
D-Phe are located are labelled (3L) and (3D), respectively.
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The above figure is
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2008,
64,
331-334)
copyright 2008.
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