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PDBsum entry 2vzk
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173 a.a.
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213 a.a.
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197 a.a.
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References listed in PDB file
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Key reference
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Title
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Anatomy of a simple acyl intermediate in enzyme catalysis: combined biophysical and modeling studies on ornithine acetyl transferase.
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Authors
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A.Iqbal,
I.J.Clifton,
M.Bagonis,
N.J.Kershaw,
C.Domene,
T.D.Claridge,
C.W.Wharton,
C.J.Schofield.
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Ref.
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J Am Chem Soc, 2009,
131,
749-757.
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PubMed id
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Abstract
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Acyl-enzyme complexes are intermediates in reactions catalyzed by many
hydrolases and related enzymes which employ nucleophilic catalysis. However,
most of the reported structural data on acyl-enzyme complexes has been acquired
under noncatalytic conditions. Recent IR analyses have indicated that some
acyl-enzyme complexes may be more flexible than most crystallographic analyses
have implied. OAT2 is a member of the N-terminal nucleophile (Ntn) hydrolase
enzyme superfamily and catalyzes the reversible transfer of an acetyl group
between the alpha-amino groups of ornithine and glutamate in a mechanism
proposed to involve an acyl-enzyme complex. We have carried out biophysical
analyses on ornithine acetyl transferase (OAT2), both in solution and in the
crystalline state. Mass spectrometric studies identified Thr-181 as the residue
acetylated during OAT2 catalysis; (13)C NMR analyses implied the presence of an
acyl-enzyme complex in solution. Crystallization of OAT2 in the presence of
N-alpha-acetyl-L-glutamate led to a structure in which Thr-181 was acetylated;
the carbonyl oxygen of the acyl-enzyme complex was located in an oxyanion hole
and positioned to hydrogen bond with the backbone amide NH of Gly-112 and the
alcohol of Thr-111. While the crystallographic analyses revealed only one
structure, IR spectroscopy demonstrated the presence of two distinct acyl-enzyme
complex structures with carbonyl stretching frequencies at 1691 and 1701 cm(-1).
Modeling studies implied two possible acyl-enzyme complex structures, one of
which correlates with that observed in the crystal structure and with the 1691
cm(-1) IR absorption. The second acyl-enzyme complex structure, which has only a
single oxyanion hole hydrogen bond, is proposed to give rise to the 1701 cm(-1)
IR absorption. The two acyl-enzyme complex structures can interconvert by
movement of the Thr-111 side-chain alcohol hydrogen away from the oxyanion hole
to hydrogen bond with the backbone carbonyl of the acylated residue, Thr-181.
Overall, the results reveal that acyl-enzyme complex structures may be more
dynamic than previously thought and support the use of a comprehensive
biophysical and modeling approach in studying such intermediates.
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Secondary reference #1
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Title
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X-Ray crystal structure of ornithine acetyltransferase from the clavulanic acid biosynthesis gene cluster.
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Authors
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J.M.Elkins,
N.J.Kershaw,
C.J.Schofield.
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Ref.
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Biochem J, 2005,
385,
565-573.
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PubMed id
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