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PDBsum entry 1qi9
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Oxidoreductase
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PDB id
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1qi9
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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X-Ray structure determination of a vanadium-Dependent haloperoxidase from ascophyllum nodosum at 2.0 a resolution.
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Authors
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M.Weyand,
H.Hecht,
M.Kiess,
M.Liaud,
H.Vilter,
D.Schomburg.
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Ref.
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J Mol Biol, 1999,
293,
595-611.
[DOI no: ]
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PubMed id
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Abstract
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The homo-dimeric structure of a vanadium-dependent haloperoxidase (V-BPO) from
the brown alga Ascophyllum nodosum (EC 1.1.11.X) has been solved by single
isomorphous replacement anomalous scattering (SIRAS) X-ray crystallography at
2.0 A resolution (PDB accession code 1QI9), using two heavy-atom datasets of a
tungstate derivative measured at two different wavelengths. The protein sequence
(SwissProt entry code P81701) of V-BPO was established by combining results from
protein and DNA sequencing, and electron density interpretation. The enzyme has
nearly an all-helical structure, with two four-helix bundles and only three
small beta-sheets. The holoenzyme contains trigonal-bipyramidal coordinated
vanadium atoms at its two active centres. Structural similarity to the only
other structurally characterized vanadium-dependent chloroperoxidase (V-CPO)
from Curvularia inaequalis exists in the vicinity of the active site and to a
lesser extent in the central four-helix bundle. Despite the low sequence and
structural similarity between V-BPO and V-CPO, the vanadium binding centres are
highly conserved on the N-terminal side of an alpha-helix and include the
proposed catalytic histidine residue (His418(V-BPO)/His404(V-CPO)). The V-BPO
structure contains, in addition, a second histidine near the active site
(His411(V-BPO)), which can alter the redox potential of the catalytically active
VO2-O2 species by protonation/deprotonation reactions. Specific binding sites
for the organic substrates, like indoles and monochlordimedone, or for halide
ions are not visible in the V-BPO structure. A reaction mechanism for the
enzymatic oxidation of halides is discussed, based on the present structural,
spectroscopic and biochemical knowledge of vanadium-dependent haloperoxidases,
explaining the observed enzymatic differences between both enzymes.
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Figure 8.
Figure 8. Structure alignment of V-CPO and V-BPO. Residues with special functions are in coloured bold letters:
green, connected to vanadium atom; red, hydrogen-bonded to vanadate oxygen atoms; catalytic active histidine resi-
dues, pink (conserved in V-HPO) and blue (unique in V-BPO). C
a
-pairs used in matrix and RMS deviation calcu-
lations are marked by asterisks (*). The tertiary structure alignment (Lessel & Schomburg, 1994) and the Figure was
prepared using BRAGI (Schomburg & Reichelt, 1988).
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Figure 10.
Figure 10. Proposal of a common
reaction mechanism for the halide
oxidation by vanadium-dependent
haloperoxidases. See Discussion.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1999,
293,
595-611)
copyright 1999.
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