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PDBsum entry 2dki
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Oxidoreductase
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PDB id
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2dki
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References listed in PDB file
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Key reference
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Title
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Crystal structure of 3-Hydroxybenzoate hydroxylase from comamonas testosteroni has a large tunnel for substrate and oxygen access to the active site.
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Authors
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T.Hiromoto,
S.Fujiwara,
K.Hosokawa,
H.Yamaguchi.
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Ref.
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J Mol Biol, 2006,
364,
878-896.
[DOI no: ]
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PubMed id
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Abstract
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The 3-hydroxybenzoate hydroxylase (MHBH) from Comamonas testosteroni KH122-3s is
a single-component flavoprotein monooxygenase, a member of the glutathione
reductase (GR) family. It catalyzes the conversion of 3-hydroxybenzoate to
3,4-dihydroxybenzoate with concomitant requirements for equimolar amounts of
NADPH and molecular oxygen. The production of dihydroxy-benzenoid derivative by
hydroxylation is the first step in the aerobic degradation of various phenolic
compounds in soil microorganisms. To establish the structural basis for
substrate recognition, the crystal structure of MHBH in complex with its
substrate was determined at 1.8 A resolution. The enzyme is shown to form a
physiologically active homodimer with crystallographic 2-fold symmetry, in which
each subunit consists of the first two domains comprising an active site and the
C-terminal domain involved in oligomerization. The protein fold of the catalytic
domains and the active-site architecture, including the FAD and
substrate-binding sites, are similar to those of 4-hydroxybenzoate hydroxylase
(PHBH) and phenol hydroxylase (PHHY), which are members of the GR family,
providing evidence that the flavoprotein aromatic hydroxylases share similar
catalytic actions for hydroxylation of the respective substrates. Structural
comparison of MHBH with the homologous enzymes suggested that a large tunnel
connecting the substrate-binding pocket to the protein surface serves for
substrate transport in this enzyme. The internal space of the large tunnel is
distinctly divided into hydrophilic and hydrophobic regions. The
characteristically stratified environment in the tunnel interior and the size of
the entrance would allow the enzyme to select its substrate by amphiphilic
nature and molecular size. In addition, the structure of the Xe-derivative at
2.5 A resolution led to the identification of a putative oxygen-binding site
adjacent to the substrate-binding pocket. The hydrophobic nature of the
xenon-binding site extends to the solvent through the tunnel, suggesting that
the tunnel could be involved in oxygen transport.
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Figure 4.
Figure 4. Stereo view of the FAD-binding site. The
substrate and FAD molecules are shown as stick models, as in
Figure 2(a). Residues around the FAD-binding site are shown as
stick models and labeled. Water molecules are indicated as red
spheres. The F[o]–F[c] omit electron-density map around the
FAD molecule is colored cyan (countered at the 4.0 σ level).
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Figure 6.
Figure 6. (a) Superposition of the C^α traces of MHBH and
PHHY (PDB entry 1PN0).^18 MHBH and PHHY are colored blue and
gray, respectively. Each molecule of 3-hydroxybenzoate and FAD
in the MHBH structure is colored purple and yellow,
respectively. For comparison with MHBH, the insertion
segment of PHHY (residues 170–210) is shown in red. (b)
The ribbon diagrams of: left, domain III (residues 453–639) of
MHBH; and right, the human peroxiredoxin, hORF6 (PDB entry
1PRX).^45 Conserved cysteine residues, Cys521 in domain III and
Cys47 located at the active site of hORF6, are shown as stick
models.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2006,
364,
878-896)
copyright 2006.
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