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PDBsum entry 4kn3
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Oxidoreductase/oxidoreductase inhibitor
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PDB id
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4kn3
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References listed in PDB file
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Key reference
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Title
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Complexes of dual-Function hemoglobin/dehaloperoxidase with substrate 2,4,6-Trichlorophenol are inhibitory and indicate binding of halophenol to compound i.
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Authors
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C.Wang,
L.L.Lovelace,
S.Sun,
J.H.Dawson,
L.Lebioda.
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Ref.
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Biochemistry, 2013,
52,
6203-6210.
[DOI no: ]
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PubMed id
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Abstract
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The hemoglobin of sea worm Amphitrite ornata, which for historical reasons is
abbreviated as DHP for dehaloperoxidase, has two physiological functions: it
binds dioxygen in the ferrous state and dehalogenates halophenols, such as
2,4,6-trichlorophenol (TCP), using hydrogen peroxide as the oxidant in the
ferric state. The crystal structures of three DHP variants (Y34N, Y34N/S91G, and
L100F) with TCP bound show two mutually exclusive modes of substrate binding.
One of them, the internal site, is deep inside the distal pocket with the
phenolic OH moiety forming a hydrogen bond to the water molecule coordinated to
the heme Fe. In this complex, the distal histidine is predominantly located in
the closed position and also forms a hydrogen bond to the phenolic hydroxide.
The second mode of TCP binding is external, at the heme edge, with the
halophenol molecule forming a lid covering the entrance to the distal cavity.
The distal histidine is in the open position and forms a hydrogen bond to the OH
group of TCP, which also hydrogen bonds to the hydroxyl of Tyr38. The distance
between the Cl4 atom of TCP and the heme Fe is 3.9 Å (nonbonding). In both
complexes, TCP molecules prevent the approach of hydrogen peroxide to the heme,
indicating that the complexes are inhibitory and implying that the substrates
must bind in an ordered fashion: hydrogen peroxide first and TCP second. Kinetic
studies confirmed the inhibition of DHP by high concentrations of TCP. The
external binding mode may resemble the interaction of TCP with Compound I, the
catalytic intermediate to which halophenols bind. The measured values of the
apparent Km for TCP were in the range of 0.3-0.8 mM, much lower than the
concentrations required to observe TCP binding in crystals. This indicates that
during catalysis TCP binds to Compound I. Mutant F21W, which likely has the
internal TCP binding site blocked, has ∼7% of the activity of wild-type DHP.
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