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PDBsum entry 1bt1

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1bt1
Jmol
Contents
Protein chains
336 a.a. *
Ligands
C2O ×2
Waters ×168
* Residue conservation analysis
PDB id:
1bt1
Name: Oxidoreductase
Title: Catechol oxidase from ipomoea batatas (sweet potatoes) in the native cu(ii)-cu(ii) state
Structure: Protein (catechol oxidase). Chain: a, b. Synonym: o-diphenol oxidase. Other_details: covalent thioether bond between h109 and c92
Source: Ipomoea batatas. Sweet potato. Organism_taxid: 4120. Organ: mature tuber
Resolution:
2.70Å     R-factor:   0.168     R-free:   0.256
Authors: T.Klabunde,C.Eicken,J.C.Sacchettini,B.Krebs
Key ref:
T.Klabunde et al. (1998). Crystal structure of a plant catechol oxidase containing a dicopper center. Nat Struct Biol, 5, 1084-1090. PubMed id: 9846879 DOI: 10.1038/4193
Date:
02-Sep-98     Release date:   02-Sep-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9ZP19  (PPO1_IPOBA) -  Polyphenol oxidase I, chloroplastic
Seq:
Struc:
496 a.a.
336 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.10.3.1  - Catechol oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 catechol + O2 = 2 1,2-benzoquinone + 2 H2O
2 × catechol
+ O(2)
= 2 × 1,2-benzoquinone
+ 2 × H(2)O
      Cofactor: Cu cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     oxidoreductase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1038/4193 Nat Struct Biol 5:1084-1090 (1998)
PubMed id: 9846879  
 
 
Crystal structure of a plant catechol oxidase containing a dicopper center.
T.Klabunde, C.Eicken, J.C.Sacchettini, B.Krebs.
 
  ABSTRACT  
 
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.
 
  Selected figure(s)  
 
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.
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.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1998, 5, 1084-1090) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

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19368383 B.T.Op't Holt, M.A.Vance, L.M.Mirica, D.E.Heppner, T.D.Stack, and E.I.Solomon (2009).
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19735457 C.Olivares, and F.Solano (2009).
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The unique enzymatic function of field bean (Dolichos lablab) D-galactose specific lectin: a polyphenol oxidase.
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19446530 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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PDB codes: 3ixv 3ixw
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Crystal structure of Manduca sexta prophenoloxidase provides insights into the mechanism of type 3 copper enzymes.
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PDB code: 3hhs
18422877 A.Brack, N.Hellmann, and H.Decker (2008).
Kinetic properties of hexameric tyrosinase from the crustacean Palinurus elephas.
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18283364 A.Prokofieva, A.I.Prikhod'ko, S.Dechert, and F.Meyer (2008).
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18279382 E.Jaenicke, and H.Decker (2008).
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17284813 A.J.Bortoluzzi, A.Neves, and N.A.Rey (2007).
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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17995596 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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Scaffolded amino acids as a close structural mimic of type-3 copper binding sites.
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16964505 K.Born, P.Comba, A.Daubinet, A.Fuchs, and H.Wadepohl (2007).
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17891425 M.Güell, and P.E.Siegbahn (2007).
Theoretical study of the catalytic mechanism of catechol oxidase.
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18021062 P.Nicholls (2007).
The oxygenase-peroxidase theory of Bach and Chodat and its modern equivalents: change and permanence in scientific thinking as shown by our understanding of the roles of water, peroxide, and oxygen in the functioning of redox enzymes.
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17476452 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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17651437 S.R.Kanade, V.L.Suhas, N.Chandra, and L.R.Gowda (2007).
Functional interaction of diphenols with polyphenol oxidase. Molecular determinants of substrate/inhibitor specificity.
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17011183 A.C.Rosenzweig, and M.H.Sazinsky (2006).
Structural insights into dioxygen-activating copper enzymes.
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16342125 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.
  Chemistry, 12, 2504-2514.  
16403014 D.Hernández-Romero, A.Sanchez-Amat, and F.Solano (2006).
A tyrosinase with an abnormally high tyrosine hydroxylase/dopa oxidase ratio.
  FEBS J, 273, 257-270.  
16795103 H.Decker, T.Schweikardt, and F.Tuczek (2006).
The first crystal structure of tyrosinase: all questions answered?
  Angew Chem Int Ed Engl, 45, 4546-4550.  
16282322 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.
  J Biol Chem, 281, 824-833.  
16832797 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.
  Chemistry, 12, 6138-6150.  
16936929 I.A.Koval, P.Gamez, C.Belle, K.Selmeczi, and J.Reedijk (2006).
Synthetic models of the active site of catechol oxidase: mechanistic studies.
  Chem Soc Rev, 35, 814-840.  
16791638 I.Bento, M.A.Carrondo, and P.F.Lindley (2006).
Reduction of dioxygen by enzymes containing copper.
  J Biol Inorg Chem, 11, 539-547.  
17893747 J.P.Piquemal, and J.Pilmé (2006).
Comments on the nature of the bonding in oxygenated dinuclear copper enzyme models.
  J Mol Struct, 764, 77-86.  
16420243 N.Wang, and D.N.Hebert (2006).
Tyrosinase maturation through the mammalian secretory pathway: bringing color to life.
  Pigment Cell Res, 19, 3.  
16501879 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.
  J Mol Evol, 62, 362-374.  
16430498 S.Halaouli, M.Asther, J.C.Sigoillot, M.Hamdi, and A.Lomascolo (2006).
Fungal tyrosinases: new prospects in molecular characteristics, bioengineering and biotechnological applications.
  J Appl Microbiol, 100, 219-232.  
16436386 Y.Matoba, T.Kumagai, A.Yamamoto, H.Yoshitsu, and M.Sugiyama (2006).
Crystallographic evidence that the dinuclear copper center of tyrosinase is flexible during catalysis.
  J Biol Chem, 281, 8981-8990.
PDB codes: 1wx2 1wx3 1wx4 1wx5 1wxc 2ahk 2ahl 2zmx
16172644 A.Jancsó, Z.Paksi, N.Jakab, B.Gyurcsik, A.Rockenbauer, and T.Gajda (2005).
Solution chemical properties and catecholase-like activity of the copper(II)-Ac-His-His-Gly-His-OH system, a relevant functional model for copper containing oxidases.
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15760341 A.M.Hall, and S.J.Orlow (2005).
Degradation of tyrosinase induced by phenylthiourea occurs following Golgi maturation.
  Pigment Cell Res, 18, 122-129.  
16388472 B.Ros, F.Thümmler, and G.Wenzel (2005).
Comparative analysis of Phytophthora infestans induced gene expression in potato cultivars with different levels of resistance.
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15968512 F.Gandía-Herrero, J.Escribano, and F.García-Carmona (2005).
Characterization of the monophenolase activity of tyrosinase on betaxanthins: the tyramine-betaxanthin/dopamine-betaxanthin pair.
  Planta, 222, 307-318.  
16006247 F.Gandía-Herrero, M.Jiménez-Atiénzar, J.Cabanes, F.García-Carmona, and J.Escribano (2005).
Evidence for a common regulation in the activation of a polyphenol oxidase by trypsin and sodium dodecyl sulfate.
  Biol Chem, 386, 601-607.  
15778083 F.García-Molina, L.G.Fenoll, J.C.Morote, P.A.García-Ruiz, J.N.Rodríguez-López, F.García-Cánovas, and J.Tudela (2005).
Opposite effects of peroxidase in the initial stages of tyrosinase-catalysed melanin biosynthesis.
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16208496 I.A.Koval, C.Belle, K.Selmeczi, C.Philouze, E.Saint-Aman, A.M.Schuitema, P.Gamez, J.L.Pierre, and J.Reedijk (2005).
Catecholase activity of a mu-hydroxodicopper(II) macrocyclic complex: structures, intermediates and reaction mechanism.
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16206836 N.Gheibi, A.A.Saboury, H.Mansuri-Torshizi, K.Haghbeen, and A.A.Moosavi-Movahedi (2005).
The inhibition effect of some n-alkyl dithiocarbamates on mushroom tyrosinase.
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Biomimetic metal-radical reactivity: aerial oxidation of alcohols, amines, aminophenols and catechols catalyzed by transition metal complexes.
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16234934 V.S.Sprakel, M.C.Feiters, W.Meyer-Klaucke, M.Klopstra, J.Brinksma, B.L.Feringa, K.D.Karlin, and R.J.Nolte (2005).
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Role of Tyr-288 at the dioxygen reduction site of cytochrome bo studied by stable isotope labeling and resonance raman spectroscopy.
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Spectroscopic characterization of the electronic changes in the active site of Streptomyces antibioticus tyrosinase upon binding of transition state analogue inhibitors.
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(+)-Larreatricin hydroxylase, an enantio-specific polyphenol oxidase from the creosote bush (Larrea tridentata).
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Cu(I)-dependent biogenesis of the galactose oxidase redox cofactor.
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Purification, characterization and molecular cloning of tyrosinase from the cephalopod mollusk, Illex argentinus.
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12377129 A.E.Todd, C.A.Orengo, and J.M.Thornton (2002).
Sequence and structural differences between enzyme and nonenzyme homologs.
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Structural basis and mechanism of the inhibition of the type-3 copper protein tyrosinase from Streptomyces antibioticus by halide ions.
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Cloning and molecular characterization of a SDS-activated tyrosinase from Marinomonas mediterranea.
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PDB code: 1k3i
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