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PDBsum entry 1yhc
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References listed in PDB file
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Key reference
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Title
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Udp-3-O-((R)-3-Hydroxymyristoyl)-N-Acetylglucosamine deacetylase functions through a general acid-Base catalyst pair mechanism.
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Authors
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M.Hernick,
H.A.Gennadios,
D.A.Whittington,
K.M.Rusche,
D.W.Christianson,
C.A.Fierke.
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Ref.
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J Biol Chem, 2005,
280,
16969-16978.
[DOI no: ]
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PubMed id
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Abstract
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UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a
zinc-dependent enzyme that catalyzes the deacetylation of
UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine to form
UDP-3-O-(R-hydroxymyristoyl)glucosamine and acetate. The structural similarity
of the active site of LpxC to metalloproteases led to the proposal that LpxC
functions via a metalloprotease-like mechanism. The pH dependence of k(cat)/Km
catalyzed by Escherichia coli and Aquifex aeolicus LpxC displayed a bell-shaped
curve (EcLpxC yields apparent pKa values of 6.4+/-0.1 and 9.1+/-0.1),
demonstrating that at least two ionizations are important for maximal activity.
Metal substitution and mutagenesis experiments suggest that the basic limb of
the pH profile is because of deprotonation of a zinc-coordinated group such as
the zinc-water molecule, whereas the acidic limb of the pH profile is caused by
protonation of either Glu78 or His265. Furthermore, the magnitude of the
activity decreases and synergy observed for the active site mutants suggest that
Glu78 and His265 act as a general acid-base catalyst pair. Crystal structures of
LpxC complexed with cacodylate or palmitate demonstrate that both Glu78 and
His265 hydrogen-bond with the same oxygen atom of the tetrahedral intermediate
and the product carboxylate. These structural features suggest that LpxC
catalyzes deacetylation by using Glu78 and His265 as a general acid-base pair
and the zinc-bound water as a nucleophile.
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Figure 2.
FIG. 2. a, structure of zinc-inhibited LpxC (Protein Data
Bank accession code 1P42 [PDB]
) (15); A, catalytic zinc ion; B, inhibitory zinc ion. b, metal
coordination interactions in the binuclear zinc cluster of
zinc-inhibited LpxC.
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Figure 3.
FIG. 3. The proposed mechanisms for LpxC using either a
single bifunctional GABC (A) or a GABC pair (B).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2005,
280,
16969-16978)
copyright 2005.
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