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PDBsum entry 6v2c
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References listed in PDB file
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Key reference
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Title
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Mechanism of catalysis by l-Asparaginase.
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Authors
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J.Lubkowski,
J.Vanegas,
W.K.Chan,
P.L.Lorenzi,
J.N.Weinstein,
S.Sukharev,
D.Fushman,
S.Rempe,
A.Anishkin,
A.Wlodawer.
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Ref.
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Biochemistry, 2020,
59,
1927-1945.
[DOI no: ]
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PubMed id
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Abstract
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Two bacterial type II l-asparaginases, from Escherichia coli and
Dickeya chrysanthemi, have played a critical role for more than 40 years
as therapeutic agents against juvenile leukemias and lymphomas. Despite a long
history of successful pharmacological applications and the apparent simplicity
of the catalytic reaction, controversies still exist regarding major steps of
the mechanism. In this report, we provide a detailed description of the reaction
catalyzed by E. coli type II l-asparaginase (EcAII). Our model was
developed on the basis of new structural and biochemical experiments combined
with previously published data. The proposed mechanism is supported by quantum
chemistry calculations based on density functional theory. We provide strong
evidence that EcAII catalyzes the reaction according to the double-displacement
(ping-pong) mechanism, with formation of a covalent intermediate. Several steps
of catalysis by EcAII are unique when compared to reactions catalyzed by other
known hydrolytic enzymes. Here, the reaction is initiated by a weak nucleophile,
threonine, without direct assistance of a general base, although a distant
general base is identified. Furthermore, tetrahedral intermediates formed during
the catalytic process are stabilized by a never previously described motif.
Although the scheme of the catalytic mechanism was developed only on the basis
of data obtained from EcAII and its variants, this novel mechanism of enzymatic
hydrolysis could potentially apply to most (and possibly all) l-asparaginases.
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