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PDBsum entry 1amp
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Hydrolase(aminopeptidase)
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PDB id
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1amp
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References listed in PDB file
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Key reference
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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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Abstract
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BACKGROUND: Aminopeptidases specifically cleave the amino-terminal residue from
polypeptide chains and are involved in the metabolism of biologically active
peptides. The family includes zinc-dependent enzymes possessing either one or
two zinc ions per active site. Structural studies providing a detailed view of
the metal environment may reveal whether the one-zinc and two-zinc enzymes
constitute structurally and mechanistically distinct subclasses, and what role
the metal ions play in the catalytic process. RESULTS: We have solved the
crystal structure of the monomeric aminopeptidase from Aeromonas proteolytica at
1.8 A resolution. The protein is folded into a single alpha/beta globular
domain. The active site contains two zinc ions (3.5 A apart) with shared ligands
and symmetrical coordination spheres. We have compared it with the related
bovine lens leucine aminopeptidase and the cobalt-containing Escherichia coli
methionine aminopeptidase. CONCLUSIONS: The environment and coordination of the
two zinc ions in A. proteolytica aminopeptidase strongly support the view that
the two metal ions constitute a co-catalytic unit and play equivalent roles
during catalysis. This conflicts with the conclusions drawn from the related
bovine leucine aminopeptidase and early biochemical studies. In addition, the
known specificity of the aminopeptidase for hydrophobic amino-terminal residues
is reflected in the hydrophobicity of the active site cleft.
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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
reprinted
by permission from Cell Press:
Structure
(1994,
2,
283-291)
copyright 1994.
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Secondary reference #1
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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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