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PDBsum entry 2nxw
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References listed in PDB file
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Key reference
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Title
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The crystal structure of phenylpyruvate decarboxylase from azospirillum brasilense at 1.5 a resolution. Implications for its catalytic and regulatory mechanism.
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Authors
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W.Versées,
S.Spaepen,
J.Vanderleyden,
J.Steyaert.
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Ref.
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Febs J, 2007,
274,
2363-2375.
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PubMed id
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Abstract
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Phenylpyruvate decarboxylase (PPDC) of Azospirillum brasilense, involved in the
biosynthesis of the plant hormone indole-3-acetic acid and the antimicrobial
compound phenylacetic acid, is a thiamine diphosphate-dependent enzyme that
catalyses the nonoxidative decarboxylation of indole- and phenylpyruvate.
Analogous to yeast pyruvate decarboxylases, PPDC is subject to allosteric
substrate activation, showing sigmoidal v versus [S] plots. The present paper
reports the crystal structure of this enzyme determined at 1.5 A resolution. The
subunit architecture of PPDC is characteristic for other members of the pyruvate
oxidase family, with each subunit consisting of three domains with an open
alpha/beta topology. An active site loop, bearing the catalytic residues His112
and His113, could not be modelled due to flexibility. The biological tetramer is
best described as an asymmetric dimer of dimers. A cysteine residue that has
been suggested as the site for regulatory substrate binding in yeast pyruvate
decarboxylase is not conserved, requiring a different mechanism for allosteric
substrate activation in PPDC. Only minor changes occur in the interactions with
the cofactors, thiamine diphosphate and Mg2+, compared to pyruvate
decarboxylase. A greater diversity is observed in the substrate binding pocket
accounting for the difference in substrate specificity. Moreover, a
catalytically important glutamate residue conserved in nearly all decarboxylases
is replaced by a leucine in PPDC. The consequences of these differences in terms
of the catalytic and regulatory mechanism of PPDC are discussed.
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