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PDBsum entry 1igb
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Aminopeptidase
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PDB id
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1igb
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References listed in PDB file
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Key reference
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Title
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The structure of the aeromonas proteolytica aminopeptidase complexed with a hydroxamate inhibitor. Involvement in catalysis of glu151 and two zinc ions of the co-Catalytic unit.
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Authors
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B.Chevrier,
H.D'Orchymont,
C.Schalk,
C.Tarnus,
D.Moras.
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Ref.
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Eur J Biochem, 1996,
237,
393-398.
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
76%.
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Abstract
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The structure of the complex of Aeromonas proteolytica aminopeptidase, a
two-zinc exopeptidase, with the inhibitor p-iodo-D-phenylalanine hydroxamate has
been determined by X-ray crystallography. Refinement of the structure, which
includes 220 water molecules, using data at 0.80-0.23-nm resolution resulted in
a crystallographic residual R value of 16%. The hydroxamate group adopts a
planar conformation whereby the two oxygen atoms interact with the zinc ions.
The N-hydroxyl group of the inhibitor is located between the two zinc ions, a
position which is close to that occupied by a water molecule in the native
structure. The carbonyl oxygen of the inhibitor binds to Zn1, which becomes
pentacoordinated while Zn2 remains tetracoordinated, in contrast to the native
protein where both zinc ions were shown to be tetracoordinated and structurally
equivalent. Interactions of the carboxylate oxygens of Glu151 with the
hydroxamate group play an important role in the stabilization of the complex.
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Secondary reference #1
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Title
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Crystal structure of aeromonas proteolytica aminopeptidase: a prototypical member of the co-Catalytic zinc enzyme family.
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Authors
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B.Chevrier,
C.Schalk,
H.D'Orchymont,
J.M.Rondeau,
D.Moras,
C.Tarnus.
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Ref.
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Structure, 1994,
2,
283-291.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. (a) Stereoview of the zinc ligands in the
metal-binding site. Dashed lines indicate the strong
zinc–ligand interactions. (b) Stereoview of the electron
density contoured at 1.5 σ level. This view emphasizes the
bidendate character of the Zn2– carboxylate interaction with
Asp179. A similar interaction is observed between Glu152 (not
labeled) and Zn1. Figure 3. (a) Stereoview of the zinc
ligands in the metal-binding site. Dashed lines indicate the
strong zinc–ligand interactions. (b) Stereoview of the
electron density contoured at 1.5 σ level. This view emphasizes
the bidendate character of the Zn2– carboxylate interaction
with Asp179. A similar interaction is observed between Glu152
(not labeled) and Zn1.
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Figure 7.
Figure 7. Histogram plotting the number of water molecules with
respect to their distance from the closest polar protein atoms.
Figure 7. Histogram plotting the number of water molecules
with respect to their distance from the closest polar protein
atoms.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #2
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Title
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Rapid purification of the aeromonas proteolytica aminopeptidase: crystallization and preliminary X-Ray data.
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Authors
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C.Schalk,
J.M.Remy,
B.Chevrier,
D.Moras,
C.Tarnus.
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Ref.
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Arch Biochem Biophys, 1992,
294,
91-97.
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PubMed id
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