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PDBsum entry 1bug
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Oxidoreductase
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PDB id
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1bug
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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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Crystal structure of a plant catechol oxidase containing a dicopper center.
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Authors
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T.Klabunde,
C.Eicken,
J.C.Sacchettini,
B.Krebs.
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Ref.
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Nat Struct Biol, 1998,
5,
1084-1090.
[DOI no: ]
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PubMed id
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Abstract
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Catechol oxidases are ubiquitous plant enzymes containing a dinuclear copper
center. In the wound-response mechanism of the plant they catalyze the oxidation
of a broad range of ortho-diphenols to the corresponding o-quinones coupled with
the reduction of oxygen to water. The crystal structures of the enzyme from
sweet potato in the resting dicupric Cu(II)-Cu(II) state, the reduced dicuprous
Cu(I)-Cu(I) form, and in complex with the inhibitor phenylthiourea were
analyzed. The catalytic copper center is accommodated in a central
four-helix-bundle located in a hydrophobic pocket close to the surface. Both
metal binding sites are composed of three histidine ligands. His 109, ligated to
the CuA site, is covalently linked to Cys 92 by an unusual thioether bond. Based
on biochemical, spectroscopic and the presented structural data, a catalytical
mechanism is proposed in which one of the oxygen atoms of the diphenolic
substrate binds to CuB of the oxygenated enzyme.
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Figure 3.
Figure 3. Active site region of catechol oxidase. a, Stereo
view of the active site region with phenylthiourea bound to the
dicopper center. The sulfur of the inhibitor binds to both
copper ions. In addition the hydrophobic cavity formed by
residues Ile 241, His 244, Phe 261 provides van der Waals
contacts with the aromatic ring of the drug. A stick
presentation of the active site residues of the resting
Cu(II)-Cu(II) state of the enzyme is superimposed in light green
to reveal the conformational change induced by the binding of
PTU. b, Presentation of the molecular surface of the hydrophobic
binding cavity of catechol oxidase showing the two metal ions,
the inhibitor, and Phe 261 in a stick presentation. The
electrostatic surface has been generated omitting these
residues. Areas colored in pink have a negative potential and
areas in purple are of positive potential. c, A close-up of the
hydrophobic binding cavity of catechol oxidase. The images have
been computed using the programs SETOR^30 and SPOCK^31.
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Figure 4.
Figure 4. Superposition of the dinuclear copper center of sweet
potato catechol oxidase with bound phenylthiourea (PTU) with the
oxygenated form of Limulus polyphemus hemocyanin^19. The side
chains of catechol oxidase are colored by atom type and the
metal-ligating histidine residues of lpHC are shown in green.
The metal-ligating residues forming the CuB binding site are
completely conserved (see also Fig. 6). For the CuA binding site
two amino acid substitutions are found. The HXXXH sequence motif
present in lpHC is changed to HXXXC^92 in catechol oxidase. In
catechol oxidase the side chain of Cys 92 is not coordinated to
CuA and the corresponding free co-ordination site is occupied by
His 109. In hemocyanin phenylalanine Phe 49, located on an  -helix
from the N-terminal domain, blocks the substrate access to the
dicopper center.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(1998,
5,
1084-1090)
copyright 1998.
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