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PDBsum entry 3hjs
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Oxidoreductase
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PDB id
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3hjs
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References listed in PDB file
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Key reference
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Title
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Catechol 1,2-Dioxygenase from the gram-Positive rhodococcus opacus 1cp: quantitative structure/activity relationship and the crystal structures of native enzyme and catechols adducts.
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Authors
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I.Matera,
M.Ferraroni,
M.Kolomytseva,
L.Golovleva,
A.Scozzafava,
F.Briganti.
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Ref.
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J Struct Biol, 2010,
170,
548-564.
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PubMed id
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Abstract
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The first crystallographic structures of a catechol 1,2-dioxygenase from a
Gram-positive bacterium Rhodococcus opacus 1CP (Rho 1,2-CTD), a Fe(III) ion
containing enzyme specialized in the aerobic biodegradation of catechols, and
its adducts with catechol, 3-methylcatechol, 4-methylcatechol, pyrogallol
(benzene-1,2,3-triol), 3-chlorocatechol, 4-chlorocatechol, 3,5-dichlorocatechol,
4,5-dichlorocatechol and protocatechuate (3,4-dihydroxybenzoate) have been
determined and analyzed. This study represents the first extensive
characterization of catechols adducts of 1,2-CTDs. The structural analyses
reveal the diverse modes of binding to the active metal iron ion of the tested
catechols thus allowing to identify the residues selectively involved in
recognition of the diverse substrates by this class of enzymes. The comparison
is further extended to the structural and functional characteristics of the
other 1,2-CTDs isolated from Gram-positive and Gram-negative bacteria. Moreover
the high structural homology of the present enzyme with the 3-chlorocatechol
1,2-dioxygenase from the same bacterium are discussed in terms of their
different substrate specificity. The catalytic rates for Rho 1,2-CTD conversion
of the tested compounds are also compared with the calculated energies of the
highest occupied molecular orbital (E(HOMO)) of the substrates. A quantitative
relationship (R=0.966) between the ln k(cat) and the calculated electronic
parameter E(HOMO) was obtained for catechol, 3-methylcatechol, 4-methylcatechol,
pyrogallol, 3-chlorocatechol, 4-chlorocatechol. This indicates that for these
substrates the rate-limiting step of the reaction cycle is dependent on their
nucleophilic reactivity. The discrepancies observed in the quantitative
relationship for 3,5-dichlorocatechol, 4,5-dichlorocatechol and protocatechuate
are ascribed to the sterical hindrances leading to the distorted binding of such
catechols observed in the corresponding structures.
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