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PDBsum entry 1bls
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Hydrolase (acting in cyclic amides)
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PDB id
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1bls
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Contents |
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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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Crystallographic structure of a phosphonate derivative of the enterobacter cloacae p99 cephalosporinase: mechanistic interpretation of a beta-Lactamase transition-State analog.
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Authors
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E.Lobkovsky,
E.M.Billings,
P.C.Moews,
J.Rahil,
R.F.Pratt,
J.R.Knox.
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Ref.
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Biochemistry, 1994,
33,
6762-6772.
[DOI no: ]
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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
96%.
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Abstract
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The crystal structure of a complex formed on reaction of the Enterobacter
cloacae P99 cephalosporinase (beta-lactamase) with a phosphonate monoester
inhibitor, m-carboxyphenyl [[N-[(p-iodophenyl)acetyl]amino]methyl]phosphonate,
has been obtained at 2.3-A resolution. The structure shows that the inhibitor
has phosphonylated the active site serine (Ser64) with loss of the
m-carboxyphenol leaving group. The inhibitor is positioned in the active site in
a way that can be interpreted in terms of a transition-state analog. The
arylacetamido side chain is placed as anticipated from analogous beta-lactamoyl
complexes of penicillin-recognizing enzymes, with the amino group
hydrogen-bonded to the backbone carbonyl of Ser318 (of the B3 beta-strand) and
to the amides of Gln120 and Asn152. There is support in the asymmetry of the
hydrogen bonding of this side chain to the protein and in the 2-fold disorder of
the benzyl group for the considerable breadth in substrate specificity exhibited
by class C beta-lactamases. One phosphonyl oxygen atom is in the oxyanion hole,
hydrogen-bonded to main-chain NH groups of Ser318 and Ser64, while the other
oxygen is solvated, not within hydrogen-bonding distance of any amino acid side
chain. The closest active site functional group to the solvated oxygen atom is
the Tyr150 hydroxyl group (3.4A); Lys67 and Lys315 are quite distant (4.3 and
5.7 A, respectively). Rather, Tyr150 and Lys67 are more closely associated with
Ser64O gamma (2.9 and 3.3 A). This arrangement is interpreted in terms of the
transition state for breakdown of the tetrahedral intermediate in the
deacylation step of catalysis, where the Tyr150 phenol seems the most likely
general acid. Thus, Tyr150, as the phenoxide anion, would be the general base
catalyst in acylation, as proposed by Oefner et al. [Nature (1990) 343,
284-288]. The structure is compared with that of a similar phosphonate
derivative of a class A beta-lactamase [Chen et al. (1993) J. Mol. Biol. 234,
165-178], and mechanistic comparisons are made. The sensitivity of serine
beta-lactamases, as opposed to serine proteinases, toward inhibition by
phosphonate monoanions is supported by electrostatic calculations showing a net
positive potential only in the catalytic sites of the beta-lactamases.
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Secondary reference #1
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Title
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Evolution of an enzyme activity: crystallographic structure at 2-A resolution of cephalosporinase from the ampc gene of enterobacter cloacae p99 and comparison with a class a penicillinase.
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Authors
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E.Lobkovsky,
P.C.Moews,
H.Liu,
H.Zhao,
J.M.Frere,
J.R.Knox.
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Ref.
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Proc Natl Acad Sci U S A, 1993,
90,
11257-11261.
[DOI no: ]
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PubMed id
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