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PDBsum entry 4znb
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structural consequences of the active site substitution cys181 ==> ser in metallo-Beta-Lactamase from bacteroides fragilis.
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Authors
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Z.Li,
B.A.Rasmussen,
O.Herzberg.
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Ref.
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Protein Sci, 1999,
8,
249-252.
[DOI no: ]
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PubMed id
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Abstract
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The metallo-beta-lactamases require divalent cations such as zinc or cadmium for
hydrolyzing the amide bond of beta-lactam antibiotics. The crystal structure of
the Zn2+ -bound enzyme from Bacteroides fragilis contains a binuclear zinc
center in the active site. A hydroxide, coordinated to both zinc atoms, is
proposed as the moiety that mounts the nucleophilic attack on the carbonyl
carbon atom of the beta-lactam bond of the substrate. It was previously reported
that the replacement of the active site Cys181 by a serine residue severely
impaired catalysis while atomic absorption measurements indicated that binding
of the two zinc ions remained intact. Contradicting data emerge from recent mass
spectrometry results, which show that only a single zinc ion binds to the C181S
metallo-beta-lactamase. In the current study, the C181S mutant enzyme was
examined at the atomic level by determining the crystal structure at 2.6 A
resolution. The overall structure of the mutant enzyme is the same as that of
the wild-type enzyme. At the mutation site, the side chain of Ser181 occupies
the same position as that of the side chain of Cys181 in the wild-type protein.
One zinc ion, Zn1, is present in the crystal structure; however, the site of the
second zinc ion, Zn2 is unoccupied. A water molecule is associated with Zn1,
reminiscent of the hydroxide seen in the structure of the wild-type enzyme but
farther from the metal. The position of the water molecule is off the plane of
the carboxylate group of Asp103; therefore, the water molecule may be less
nucleophilic than a water molecule which is coplanar with the carboxylate group.
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Secondary reference #1
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Title
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Crystal structures of the cadmium- And mercury-Substituted metallo-Beta-Lactamase from bacteroides fragilis.
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Authors
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N.O.Concha,
B.A.Rasmussen,
K.Bush,
O.Herzberg.
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Ref.
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Protein Sci, 1997,
6,
2671-2676.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Proposed catalytic mechanism for the binuclear-center metallo-P-lactamases
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Figure 3.
Fig. 3. Active site of the Hgz+-soaked crystal structure. A: density map a1 the region of the active site. The coefficients
ZF, ~ F, and calculated phases are used. The map is contoured at I cr level. B: Superposition of' the Hg2+ and Zn2+ binuclear centers
and their environments (solid and broken lines, respectively). Zinc and mercury ions of the Hg2+-bound structure are shown as
circles, and the zinc ions and associated solvent r the Zn'+-bound structure are shown as open circles. Wat 1 corresponds to
hydroxide.
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by the Protein Society
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Secondary reference #2
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Title
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Crystal structure of the wide-Spectrum binuclear zinc beta-Lactamase from bacteroides fragilis.
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Authors
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N.O.Concha,
B.A.Rasmussen,
K.Bush,
O.Herzberg.
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Ref.
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Structure, 1996,
4,
823-836.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2. The active site of the B. fragilis
metallo-β-lactamase. The molecular surface of the enzyme is
depicted together with a model of a bound molecule of
benzylpenicillin (colored red). The benzyl side chain fits into
a hydrophobic pocket. The zinc ions are represented as magenta
spheres and two key water molecules as blue spheres. The
disordered residues, 48 and 49, and the side chain of Glu50 are
colored light blue. (The figure was generated with GRASP [72]).
Figure 2. The active site of the B. fragilis
metallo-β-lactamase. The molecular surface of the enzyme is
depicted together with a model of a bound molecule of
benzylpenicillin (colored red). The benzyl side chain fits into
a hydrophobic pocket. The zinc ions are represented as magenta
spheres and two key water molecules as blue spheres. The
disordered residues, 48 and 49, and the side chain of Glu50 are
colored light blue. (The figure was generated with GRASP
[[3]72]).
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Figure 6.
Figure 6. Models of β-lactam substrates bound in the active
site of the metallo-β-lactamase from B. fragilis. The
substrates, shown in magenta, are: (a) ampicillin, (b)
ceftazidime and (c) imipenem. The corresponding chemical
structures are displayed on the right. The coloring scheme is as
described in the legend of Figure 3a. In addition, the dark
blue dotted line shows the shared hydroxide's proposed line of
attack on the carbonyl carbon of the substrate. Figure 6.
Models of β-lactam substrates bound in the active site of the
metallo-β-lactamase from B. fragilis. The substrates, shown in
magenta, are: (a) ampicillin, (b) ceftazidime and (c) imipenem.
The corresponding chemical structures are displayed on the
right. The coloring scheme is as described in the legend of
[5]Figure 3a. In addition, the dark blue dotted line shows the
shared hydroxide's proposed line of attack on the carbonyl
carbon of the substrate.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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