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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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* Residue conservation analysis
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Enzyme class:
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E.C.1.10.3.1
- catechol oxidase.
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Reaction:
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2 catechol + O2 = 2 1,2-benzoquinone + 2 H2O
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2
×
catechol
Bound ligand (Het Group name = )
matches with 50.00% similarity
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+
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O2
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=
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2
×
1,2-benzoquinone
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+
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2
×
H2O
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Cofactor:
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Cu cation
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Nat Struct Biol
5:1084-1090
(1998)
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PubMed id:
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Crystal structure of a plant catechol oxidase containing a dicopper center.
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T.Klabunde,
C.Eicken,
J.C.Sacchettini,
B.Krebs.
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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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Selected figure(s)
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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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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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F.G.Mutti,
M.Gullotti,
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(2011).
A new chiral, poly-imidazole N8-ligand and the related di- and tri-copper(II) complexes: synthesis, theoretical modelling, spectroscopic properties, and biomimetic stereoselective oxidations.
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Dalton Trans,
40,
5436-5457.
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J.Liu,
F.Wu,
L.Chen,
J.Hu,
L.Zhao,
C.Chen,
and
L.Peng
(2011).
Evaluation of dihydropyrimidin-(2H)-one analogues and rhodanine derivatives as tyrosinase inhibitors.
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Bioorg Med Chem Lett,
21,
2376-2379.
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V.L.Davidson
(2011).
Generation of protein-derived redox cofactors by posttranslational modification.
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Mol Biosyst,
7,
29-37.
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Y.M.Ha,
J.Y.Park,
Y.J.Park,
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Y.J.Choi,
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Y.K.Han,
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H.R.Moon,
and
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(2011).
Synthesis and biological activity of hydroxy substituted phenyl-benzo[d]thiazole analogues for antityrosinase activity in B16 cells.
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Bioorg Med Chem Lett,
21,
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Y.Sun,
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and
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Alternative splicing in the coding region of Ppo-A1 directly influences the polyphenol oxidase activity in common wheat (Triticum aestivum L.).
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Funct Integr Genomics,
11,
85-93.
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C.Gasparetti,
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(2010).
Discovery of a new tyrosinase-like enzyme family lacking a C-terminally processed domain: production and characterization of an Aspergillus oryzae catechol oxidase.
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Appl Microbiol Biotechnol,
86,
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C.Núñez,
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and
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(2010).
Structural, MALDI-TOF-MS, magnetic and spectroscopic studies of new dinuclear copper(II), cobalt(II) and zinc(II) complexes containing a biomimicking μ-OH bridge.
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Dalton Trans,
39,
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H.Choi,
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and
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1-(4-Hy-droxy-phen-yl)-3-(3,4,5-tri-methoxy-phen-yl)thio-urea.
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Acta Crystallogr Sect E Struct Rep Online,
66,
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H.Choi,
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and
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1-(2-Hy-droxy-eth-yl)-3-(3-meth-oxy-phen-yl)thio-urea.
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Acta Crystallogr Sect E Struct Rep Online,
66,
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J.A.Worrall,
and
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Copper mining in Streptomyces: enzymes, natural products and development.
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Nat Prod Rep,
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Suicide inactivation of the diphenolase and monophenolase activities of tyrosinase.
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IUBMB Life,
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M.Fairhead,
and
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Role of the C-terminal extension in a bacterial tyrosinase.
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FEBS J,
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R.K.Das,
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Bimetallic catalysis involving dipalladium(I) and diruthenium(I) complexes.
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Chemistry,
16,
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B.T.Op't Holt,
M.A.Vance,
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and
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Reaction coordinate of a functional model of tyrosinase: spectroscopic and computational characterization.
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J Am Chem Soc,
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C.Olivares,
and
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New insights into the active site structure and catalytic mechanism of tyrosinase and its related proteins.
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Pigment Cell Melanoma Res,
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J.Yoon,
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Geometric and electronic structure differences between the type 3 copper sites of the multicopper oxidases and hemocyanin/tyrosinase.
|
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Proc Natl Acad Sci U S A,
106,
6585-6590.
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S.R.Kanade,
D.H.Rao,
R.N.Hegde,
and
L.R.Gowda
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The unique enzymatic function of field bean (Dolichos lablab) D-galactose specific lectin: a polyphenol oxidase.
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Glycoconj J,
26,
535-545.
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Y.Cong,
Q.Zhang,
D.Woolford,
T.Schweikardt,
H.Khant,
M.Dougherty,
S.J.Ludtke,
W.Chiu,
and
H.Decker
(2009).
Structural mechanism of SDS-induced enzyme activity of scorpion hemocyanin revealed by electron cryomicroscopy.
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Structure,
17,
749-758.
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PDB codes:
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Y.Li,
Y.Wang,
H.Jiang,
and
J.Deng
(2009).
Crystal structure of Manduca sexta prophenoloxidase provides insights into the mechanism of type 3 copper enzymes.
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Proc Natl Acad Sci U S A,
106,
17002-17006.
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PDB code:
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A.Brack,
N.Hellmann,
and
H.Decker
(2008).
Kinetic properties of hexameric tyrosinase from the crustacean Palinurus elephas.
|
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Photochem Photobiol,
84,
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A.Prokofieva,
A.I.Prikhod'ko,
S.Dechert,
and
F.Meyer
(2008).
Selective benzylic C-C coupling catalyzed by a bioinspired dicopper complex.
|
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Chem Commun (Camb),
(),
1005-1007.
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E.J.Land,
C.A.Ramsden,
P.A.Riley,
and
M.R.Stratford
(2008).
Evidence consistent with the requirement of cresolase activity for suicide inactivation of tyrosinase.
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Tohoku J Exp Med,
216,
231-238.
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E.Jaenicke,
and
H.Decker
(2008).
Kinetic properties of catecholoxidase activity of tarantula hemocyanin.
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FEBS J,
275,
1518-1528.
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E.Mijangos,
J.Reedijk,
and
L.Gasque
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Copper(ii) complexes of a polydentate imidazole-based ligand. pH effect on magnetic coupling and catecholase activity.
|
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Dalton Trans,
(),
1857-1863.
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F.G.Mutti,
R.Pievo,
M.Sgobba,
M.Gullotti,
and
L.Santagostini
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Biomimetic modeling of copper complexes: a study of enantioselective catalytic oxidation on d-(+)-catechin and L-( - )-epicatechin with copper complexes.
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Bioinorg Chem Appl,
(),
762029.
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L.B.Davin,
M.Jourdes,
A.M.Patten,
K.W.Kim,
D.G.Vassão,
and
N.G.Lewis
(2008).
Dissection of lignin macromolecular configuration and assembly: Comparison to related biochemical processes in allyl/propenyl phenol and lignan biosynthesis.
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Nat Prod Rep,
25,
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M.Cammarata,
V.Arizza,
C.Cianciolo,
D.Parrinello,
M.Vazzana,
A.Vizzini,
G.Salerno,
and
N.Parrinello
(2008).
The prophenoloxidase system is activated during the tunic inflammatory reaction of Ciona intestinalis.
|
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Cell Tissue Res,
333,
481-492.
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Q.Michard,
S.Commo,
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and
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TRP-2 expression protects HEK cells from dopamine- and hydroquinone-induced toxicity.
|
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Free Radic Biol Med,
45,
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S.Hirota,
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M.Beltramini,
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N.Tanaka,
S.Nagao,
and
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(2008).
Molecular basis of the bohr effect in arthropod hemocyanin.
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J Biol Chem,
283,
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S.J.Smith,
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G.Schenk,
L.R.Gahan,
and
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Structural and spectroscopic studies of a model for catechol oxidase.
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J Biol Inorg Chem,
13,
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Y.Tatara,
T.Namba,
Y.Yamagata,
T.Yoshida,
T.Uchida,
and
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(2008).
Acid activation of protyrosinase from Aspergillus oryzae: homo-tetrameric protyrosinase is converted to active dimers with an essential intersubunit disulfide bond at acidic pH.
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Pigment Cell Melanoma Res,
21,
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2-{[Bis(2-pyridylmethyl)amino]methyl}-6-[(2-hydroxyanilino)methyl]-4-methylphenol: a novel binucleating asymmetric ligand as a precursor to synthetic models for metalloenzymes.
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Acta Crystallogr C,
63,
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E.Arias,
J.González,
R.Oria,
and
P.Lopez-Buesa
(2007).
Ascorbic acid and 4-hexylresorcinol effects on pear PPO and PPO catalyzed browning reaction.
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J Food Sci,
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Chem Commun (Camb),
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J.L.Munoz-Munoz,
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F.Garcia-Canovas,
and
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(2007).
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M.Güell,
and
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(2007).
Theoretical study of the catalytic mechanism of catechol oxidase.
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J Biol Inorg Chem,
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Biochemistry (Mosc),
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S.Bergmann,
J.Markl,
and
B.Lieb
(2007).
The first complete cDNA sequence of the hemocyanin from a bivalve, the protobranch Nucula nucleus.
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J Mol Evol,
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S.R.Kanade,
V.L.Suhas,
N.Chandra,
and
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(2007).
Functional interaction of diphenols with polyphenol oxidase. Molecular determinants of substrate/inhibitor specificity.
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FEBS J,
274,
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A.C.Rosenzweig,
and
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(2006).
Structural insights into dioxygen-activating copper enzymes.
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Curr Opin Struct Biol,
16,
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A.Granata,
E.Monzani,
L.Bubacco,
and
L.Casella
(2006).
Mechanistic insight into the activity of tyrosinase from variable-temperature studies in an aqueous/organic solvent.
|
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Chemistry,
12,
2504-2514.
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D.Hernández-Romero,
A.Sanchez-Amat,
and
F.Solano
(2006).
A tyrosinase with an abnormally high tyrosine hydroxylase/dopa oxidase ratio.
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FEBS J,
273,
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H.Decker,
T.Schweikardt,
and
F.Tuczek
(2006).
The first crystal structure of tyrosinase: all questions answered?
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Angew Chem Int Ed Engl,
45,
4546-4550.
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H.Suzuki,
Y.Furusho,
T.Higashi,
Y.Ohnishi,
and
S.Horinouchi
(2006).
A novel o-aminophenol oxidase responsible for formation of the phenoxazinone chromophore of grixazone.
|
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J Biol Chem,
281,
824-833.
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I.A.Koval,
K.Selmeczi,
C.Belle,
C.Philouze,
E.Saint-Aman,
I.Gautier-Luneau,
A.M.Schuitema,
M.van Vliet,
P.Gamez,
O.Roubeau,
M.Lüken,
B.Krebs,
M.Lutz,
A.L.Spek,
J.L.Pierre,
and
J.Reedijk
(2006).
Catecholase activity of a copper(II) complex with a macrocyclic ligand: unraveling catalytic mechanisms.
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Chemistry,
12,
6138-6150.
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I.A.Koval,
P.Gamez,
C.Belle,
K.Selmeczi,
and
J.Reedijk
(2006).
Synthetic models of the active site of catechol oxidase: mechanistic studies.
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Chem Soc Rev,
35,
814-840.
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I.Bento,
M.A.Carrondo,
and
P.F.Lindley
(2006).
Reduction of dioxygen by enzymes containing copper.
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J Biol Inorg Chem,
11,
539-547.
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J.P.Piquemal,
and
J.Pilmé
(2006).
Comments on the nature of the bonding in oxygenated dinuclear copper enzyme models.
|
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J Mol Struct,
764,
77-86.
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N.Wang,
and
D.N.Hebert
(2006).
Tyrosinase maturation through the mammalian secretory pathway: bringing color to life.
|
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Pigment Cell Res,
19,
3.
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S.Bergmann,
B.Lieb,
P.Ruth,
and
J.Markl
(2006).
The hemocyanin from a living fossil, the cephalopod Nautilus pompilius: protein structure, gene organization, and evolution.
|
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J Mol Evol,
62,
362-374.
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