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Oxidoreductase PDB id
1a65
Jmol
Contents
Protein chain
504 a.a. *
Ligands
NAG
PYE
__O
Metals
_CU ×3
Waters ×296
* Residue conservation analysis
PDB id:
1a65
Name: Oxidoreductase
Title: Type-2 cu-depleted laccase from coprinus cinereus
Structure: Laccase. Chain: a. Engineered: yes
Source: Coprinopsis cinerea. Organism_taxid: 5346. Expressed in: aspergillus oryzae. Expression_system_taxid: 5062
Resolution:
2.23Å     R-factor:   0.160     R-free:   0.220
Authors: V.Ducros,W.Brzozowski
Key ref: V.Ducros et al. (1998). Crystal structure of the type-2 Cu depleted laccase from Coprinus cinereus at 2.2 A resolution. Nat Struct Biol, 5, 310-316. PubMed id: 9546223 DOI: 10.1038/nsb0498-310
Date:
05-Mar-98     Release date:   30-Mar-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9Y780  (Q9Y780_COPCI) -  Laccase 1
Seq:
Struc: 		 
Seq:
Struc: 		539 a.a.
505 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.10.3.2  - Laccase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4 benzenediol + O2 = 4 benzosemiquinone + 2 H2O
4 × benzenediol
Bound ligand (Het Group name = NAG)
matches with 57.14% similarity 		+ O(2)
 = 4 × benzosemiquinone
 + 2 × H(2)O
      Cofactor: Copper
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1038/nsb0498-310 Nat Struct Biol 5:310-316 (1998)
PubMed id: 9546223  
 
 
Crystal structure of the type-2 Cu depleted laccase from Coprinus cinereus at 2.2 A resolution.
V.Ducros, A.M.Brzozowski, K.S.Wilson, S.H.Brown, P.Ostergaard, P.Schneider, D.S.Yaver, A.H.Pedersen, G.J.Davies.
 
  ABSTRACT  
 
Laccase catalyses the oxidation of a variety of organic substrates coupled to the reduction of oxygen to water. It is widely believed to be the simplest representative of the ubiquitous blue multi-copper oxidase family. Laccase is implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism in fungi and plants. The structure of laccase from the fungus Coprinus cinereus has been determined by X-ray crystallography at a resolution of 2.2 A. Laccase is a monomer composed of three cupredoxin-like beta-sandwich domains, similar to that found in ascorbate oxidase. In contrast to ascorbate oxidase, however, the mononuclear type-1 Cu site lacks the axial methionine ligand and so exhibits trigonal planar coordination, consistent with its elevated redox potential. Crucially, the structure is trapped in a Cu depleted form in which the putative type-2 Cu atom is completely absent, but in which the remaining type-1 and type-3 Cu sites display full occupancy. Type-2 Cu depletion has unexpected consequences for the coordination of the remaining type-3 Cu atoms.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21298193 F.G.Mutti, M.Gullotti, L.Casella, L.Santagostini, R.Pagliarin, K.K.Andersson, M.F.Iozzi, and G.Zoppellaro (2011).
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21063888 P.V.Turlapati, K.W.Kim, L.B.Davin, and N.G.Lewis (2011).
The laccase multigene family in Arabidopsis thaliana: towards addressing the mystery of their gene function(s).
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21204882 S.J.Huang, Z.M.Liu, X.L.Huang, L.Q.Guo, and J.F.Lin (2011).
Molecular cloning and characterization of a novel laccase gene from a white-rot fungus Polyporus grammocephalus TR16 and expression in Pichia pastoris.
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21076916 X.Liu, M.Gillespie, A.D.Ozel, E.Dikici, S.Daunert, and L.G.Bachas (2011).
Electrochemical properties and temperature dependence of a recombinant laccase from Thermus thermophilus.
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20175122 T.K.Lundell, M.R.Mäkelä, and K.Hildén (2010).
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20200715 Z.Chen, P.Durão, C.S.Silva, M.M.Pereira, S.Todorovic, P.Hildebrandt, I.Bento, P.F.Lindley, and L.O.Martins (2010).
The role of Glu498 in the dioxygen reactivity of CotA-laccase from Bacillus subtilis.
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18581264 D.W.Wong (2009).
Structure and action mechanism of ligninolytic enzymes.
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19346471 J.Yoon, S.Fujii, and E.I.Solomon (2009).
Geometric and electronic structure differences between the type 3 copper sites of the multicopper oxidases and hemocyanin/tyrosinase.
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19360388 K.Hildén, T.K.Hakala, and T.Lundell (2009).
Thermotolerant and thermostable laccases.
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19780817 M.Andberg, N.Hakulinen, S.Auer, M.Saloheimo, A.Koivula, J.Rouvinen, and K.Kruus (2009).
Essential role of the C-terminus in Melanocarpus albomyces laccase for enzyme production, catalytic properties and structure.
  FEBS J, 276, 6285-6300.
PDB code: 3dkh
19715303 M.Choi, N.Sukumar, A.Liu, and V.L.Davidson (2009).
Defining the role of the axial ligand of the type 1 copper site in amicyanin by replacement of methionine with leucine.
  Biochemistry, 48, 9174-9184.
PDB codes: 3ie9 3iea
19282479 S.Ghosh, X.Xie, A.Dey, Y.Sun, C.P.Scholes, and E.I.Solomon (2009).
Thermodynamic equilibrium between blue and green copper sites and the role of the protein in controlling function.
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19224923 T.J.Lawton, L.A.Sayavedra-Soto, D.J.Arp, and A.C.Rosenzweig (2009).
Crystal structure of a two-domain multicopper oxidase: IMPLICATIONS FOR THE EVOLUTION OF MULTICOPPER BLUE PROTEINS.
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PDB code: 3g5w
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Metal complexes of amino acids and amino acid side chain groups. Structures and properties.
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19221878 Z.Haibo, Z.Yinglong, H.Feng, G.Peiji, and C.Jiachuan (2009).
Purification and characterization of a thermostable laccase with unique oxidative characteristics from Trametes hirsuta.
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19019256 A.Kunamneni, S.Camarero, C.García-Burgos, F.J.Plou, A.Ballesteros, and M.Alcalde (2008).
Engineering and Applications of fungal laccases for organic synthesis.
  Microb Cell Fact, 7, 32.  
18443781 G.Bleve, C.Lezzi, G.Mita, P.Rampino, C.Perrotta, L.Villanova, and F.Grieco (2008).
Molecular cloning and heterologous expression of a laccase gene from Pleurotus eryngii in free and immobilized Saccharomyces cerevisiae cells.
  Appl Microbiol Biotechnol, 79, 731-741.  
18292878 M.A.Tadesse, A.D'Annibale, C.Galli, P.Gentili, and F.Sergi (2008).
An assessment of the relative contributions of redox and steric issues to laccase specificity towards putative substrates.
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18165683 R.Wiener, Y.Haitin, L.Shamgar, M.C.Fernández-Alonso, A.Martos, O.Chomsky-Hecht, G.Rivas, B.Attali, and J.A.Hirsch (2008).
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  J Biol Chem, 283, 5815-5830.
PDB code: 3bj4
17918839 J.Yoon, and E.I.Solomon (2007).
Electronic structure of the peroxy intermediate and its correlation to the native intermediate in the multicopper oxidases: insights into the reductive cleavage of the o-o bond.
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17867686 L.M.Brines, J.Shearer, J.K.Fender, D.Schweitzer, S.C.Shoner, D.Barnhart, W.Kaminsky, S.Lovell, and J.A.Kovacs (2007).
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17897461 M.Ferraroni, N.M.Myasoedova, V.Schmatchenko, A.A.Leontievsky, L.A.Golovleva, A.Scozzafava, and F.Briganti (2007).
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  BMC Struct Biol, 7, 60.
PDB code: 2qt6
18021071 O.V.Morozova, G.P.Shumakovich, M.A.Gorbacheva, S.V.Shleev, and A.I.Yaropolov (2007).
"Blue" laccases.
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17101662 S.R.Waterman, M.Hacham, J.Panepinto, G.Hu, S.Shin, and P.R.Williamson (2007).
Cell wall targeting of laccase of Cryptococcus neoformans during infection of mice.
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16740638 A.Beloqui, M.Pita, J.Polaina, A.Martínez-Arias, O.V.Golyshina, M.Zumárraga, M.M.Yakimov, H.García-Arellano, M.Alcalde, V.M.Fernández, K.Elborough, J.M.Andreu, A.Ballesteros, F.J.Plou, K.N.Timmis, M.Ferrer, and P.N.Golyshin (2006).
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16317711 A.Marjasvaara, K.Kruus, and P.Vainiotalo (2006).
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16944230 A.V.Lyashenko, I.Bento, V.N.Zaitsev, N.E.Zhukhlistova, Y.N.Zhukova, A.G.Gabdoulkhakov, E.Y.Morgunova, W.Voelter, G.S.Kachalova, E.V.Stepanova, O.V.Koroleva, V.S.Lamzin, V.I.Tishkov, C.Betzel, P.F.Lindley, and A.M.Mikhailov (2006).
X-ray structural studies of the fungal laccase from Cerrena maxima.
  J Biol Inorg Chem, 11, 963-973.  
  17012782 A.V.Lyashenko, N.E.Zhukhlistova, A.G.Gabdoulkhakov, Y.N.Zhukova, W.Voelter, V.N.Zaitsev, I.Bento, E.V.Stepanova, G.S.Kachalova, O.V.Koroleva, E.A.Cherkashyn, V.I.Tishkov, V.S.Lamzin, K.Schirwitz, E.Y.Morgunova, C.Betzel, P.F.Lindley, and A.M.Mikhailov (2006).
Purification, crystallization and preliminary X-ray study of the fungal laccase from Cerrena maxima.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 954-957.
PDB code: 2h5u
16472305 P.Baldrian (2006).
Fungal laccases - occurrence and properties.
  FEMS Microbiol Rev, 30, 215-242.  
16650005 P.J.Hoegger, S.Kilaru, T.Y.James, J.R.Thacker, and U.Kües (2006).
Phylogenetic comparison and classification of laccase and related multicopper oxidase protein sequences.
  FEBS J, 273, 2308-2326.  
16775746 S.Kilaru, P.J.Hoegger, and U.Kües (2006).
The laccase multi-gene family in Coprinopsis cinerea has seventeen different members that divide into two distinct subfamilies.
  Curr Genet, 50, 45-60.  
16391148 S.Sakasegawa, H.Ishikawa, S.Imamura, H.Sakuraba, S.Goda, and T.Ohshima (2006).
Bilirubin oxidase activity of Bacillus subtilis CotA.
  Appl Environ Microbiol, 72, 972-975.  
16230618 A.B.Taylor, C.S.Stoj, L.Ziegler, D.J.Kosman, and P.J.Hart (2005).
The copper-iron connection in biology: structure of the metallo-oxidase Fet3p.
  Proc Natl Acad Sci U S A, 102, 15459-15464.
PDB code: 1zpu
16231129 G.Battistuzzi, M.Bellei, A.Leonardi, R.Pierattelli, A.De Candia, A.J.Vila, and M.Sola (2005).
Reduction thermodynamics of the T1 Cu site in plant and fungal laccases.
  J Biol Inorg Chem, 10, 867-873.  
16234932 I.Bento, L.O.Martins, G.Gato Lopes, M.Arménia Carrondo, and P.F.Lindley (2005).
Dioxygen reduction by multi-copper oxidases; a structural perspective.
  Dalton Trans, 0, 3507-3513.
PDB codes: 1w6l 1w6w 1w8e 2bhf
  16510995 M.Ferraroni, I.Duchi, N.M.Myasoedova, A.A.Leontievsky, L.A.Golovleva, A.Scozzafava, and F.Briganti (2005).
Crystallization and preliminary structure analysis of the blue laccase from the ligninolytic fungus Panus tigrinus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 205-207.  
15854824 S.Shleev, J.Tkac, A.Christenson, T.Ruzgas, A.I.Yaropolov, J.W.Whittaker, and L.Gorton (2005).
Direct electron transfer between copper-containing proteins and electrodes.
  Biosens Bioelectron, 20, 2517-2554.  
16332742 Y.Taprab, T.Johjima, Y.Maeda, S.Moriya, S.Trakulnaleamsai, N.Noparatnaraporn, M.Ohkuma, and T.Kudo (2005).
Symbiotic fungi produce laccases potentially involved in phenol degradation in fungus combs of fungus-growing termites in Thailand.
  Appl Environ Microbiol, 71, 7696-7704.  
15468136 A.Marjasvaara, M.Torvinen, and P.Vainiotalo (2004).
Laccase-catalyzed mediated oxidation of benzyl alcohol: the role of TEMPO and formation of products including benzonitrile studied by nanoelectrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.
  J Mass Spectrom, 39, 1139-1146.  
14764581 F.J.Enguita, D.Marçal, L.O.Martins, R.Grenha, A.O.Henriques, P.F.Lindley, and M.A.Carrondo (2004).
Substrate and dioxygen binding to the endospore coat laccase from Bacillus subtilis.
  J Biol Chem, 279, 23472-23476.
PDB codes: 1hkz 1uvw
15308236 F.Vianello, A.Cambria, S.Ragusa, M.T.Cambria, L.Zennaro, and A.Rigo (2004).
A high sensitivity amperometric biosensor using a monomolecular layer of laccase as biorecognition element.
  Biosens Bioelectron, 20, 315-321.  
12637519 F.J.Enguita, L.O.Martins, A.O.Henriques, and M.A.Carrondo (2003).
Crystal structure of a bacterial endospore coat component. A laccase with enhanced thermostability properties.
  J Biol Chem, 278, 19416-19425.
PDB code: 1gsk
14532088 L.F.Larrondo, L.Salas, F.Melo, R.Vicuña, and D.Cullen (2003).
A novel extracellular multicopper oxidase from Phanerochaete chrysosporium with ferroxidase activity.
  Appl Environ Microbiol, 69, 6257-6263.  
12800133 S.V.Kumar, P.S.Phale, S.Durani, and P.P.Wangikar (2003).
Combined sequence and structure analysis of the fungal laccase family.
  Biotechnol Bioeng, 83, 386-394.  
12009907 A.E.Palmer, L.Quintanar, S.Severance, T.P.Wang, D.J.Kosman, and E.I.Solomon (2002).
Spectroscopic characterization and O2 reactivity of the trinuclear Cu cluster of mutants of the multicopper oxidase Fet3p.
  Biochemistry, 41, 6438-6448.  
12473107 A.Klonowska, C.Gaudin, A.Fournel, M.Asso, J.Le Petit, M.Giorgi, and T.Tron (2002).
Characterization of a low redox potential laccase from the basidiomycete C30.
  Eur J Biochem, 269, 6119-6125.  
11872481 A.P.Litvintseva, and J.M.Henson (2002).
Cloning, characterization, and transcription of three laccase genes from Gaeumannomyces graminis var. tritici, the take-all fungus.
  Appl Environ Microbiol, 68, 1305-1311.  
11856319 E.Record, P.J.Punt, M.Chamkha, M.Labat, C.A.van Den Hondel, and M.Asther (2002).
Expression of the Pycnoporus cinnabarinus laccase gene in Aspergillus niger and characterization of the recombinant enzyme.
  Eur J Biochem, 269, 602-609.  
12115407 F.Hong, N.Q.Meinander, and L.J.Jönsson (2002).
Fermentation strategies for improved heterologous expression of laccase in Pichia pastoris.
  Biotechnol Bioeng, 79, 438-449.  
12163489 K.Piontek, M.Antorini, and T.Choinowski (2002).
Crystal structure of a laccase from the fungus Trametes versicolor at 1.90-A resolution containing a full complement of coppers.
  J Biol Chem, 277, 37663-37669.
PDB code: 1gyc
11884407 L.O.Martins, C.M.Soares, M.M.Pereira, M.Teixeira, T.Costa, G.H.Jones, and A.O.Henriques (2002).
Molecular and biochemical characterization of a highly stable bacterial laccase that occurs as a structural component of the Bacillus subtilis endospore coat.
  J Biol Chem, 277, 18849-18859.  
12118243 N.Hakulinen, L.L.Kiiskinen, K.Kruus, M.Saloheimo, A.Paananen, A.Koivula, and J.Rouvinen (2002).
Crystal structure of a laccase from Melanocarpus albomyces with an intact trinuclear copper site.
  Nat Struct Biol, 9, 601-605.
PDB code: 1gw0
12177070 P.Vachette, E.Dainese, V.B.Vasyliev, P.Di Muro, M.Beltramini, D.I.Svergun, V.De Filippis, and B.Salvato (2002).
A key structural role for active site type 3 copper ions in human ceruloplasmin.
  J Biol Chem, 277, 40823-40831.  
11867755 S.A.Roberts, A.Weichsel, G.Grass, K.Thakali, J.T.Hazzard, G.Tollin, C.Rensing, and W.R.Montfort (2002).
Crystal structure and electron transfer kinetics of CueO, a multicopper oxidase required for copper homeostasis in Escherichia coli.
  Proc Natl Acad Sci U S A, 99, 2766-2771.
PDB code: 1kv7
12044164 T.Bertrand, C.Jolivalt, P.Briozzo, E.Caminade, N.Joly, C.Madzak, and C.Mougin (2002).
Crystal structure of a four-copper laccase complexed with an arylamine: insights into substrate recognition and correlation with kinetics.
  Biochemistry, 41, 7325-7333.
PDB code: 1kya
  12489775 V.Shah, and F.Nerud (2002).
Lignin degrading system of white-rot fungi and its exploitation for dye decolorization.
  Can J Microbiol, 48, 857-870.  
11170402 A.Donaire, B.Jiménez, J.Moratal, J.F.Hall, and S.S.Hasnain (2001).
Electronic characterization of the oxidized state of the blue copper protein rusticyanin by 1H NMR: is the axial methionine the dominant influence for the high redox potential?
  Biochemistry, 40, 837-846.  
11466290 C.Kim, W.W.Lorenz, J.T.Hoopes, and J.F.Dean (2001).
Oxidation of phenolate siderophores by the multicopper oxidase encoded by the Escherichia coli yacK gene.
  J Bacteriol, 183, 4866-4875.  
12404359 E.I.Solomon, P.Chen, M.Metz, S.K.Lee, and A.E.Palmer (2001).
Oxygen Binding, Activation, and Reduction to Water by Copper Proteins.
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16233113 H.Hoshida, M.Nakao, H.Kanazawa, K.Kubo, T.Hakukawa, K.Morimasa, R.Akada, and Y.Nishizawa (2001).
Isolation of five laccase gene sequences from the white-rot fungus Trametes sanguinea by PCR, and cloning, characterization and expression of the laccase cDNA in yeasts.
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11282346 W.B.Tolman, and D.J.Spencer (2001).
New advances in ligand design for synthetic modeling of metalloprotein active sites.
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Laccases are widespread in bacteria.
  Trends Biotechnol, 18, 41-42.  
  10941525 L.Otterbein, E.Record, D.Chereau, I.Herpoël, M.Asther, and S.M.Moukha (2000).
Isolation of a new laccase isoform from the white-rot fungi Pycnoporus cinnabarinus strain ss3.
  Can J Microbiol, 46, 759-763.  
10712591 L.Otterbein, E.Record, S.Longhi, M.Asther, and S.Moukha (2000).
Molecular cloning of the cDNA encoding laccase from Pycnoporus cinnabarinus I-937 and expression in Pichia pastoris.
  Eur J Biochem, 267, 1619-1625.  
10642183 M.J.Colaneri, J.Vitali, and J.Peisach (2000).
Electron spin-echo envelope modulation study of multicrystalline Cu(2+)-insulin: effects of Cd(2+) on the nuclear quadrupole interaction of the Cu(2+)-coordinated imidazole remote nitrogen.
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10694398 N.J.Blackburn, M.Ralle, R.Hassett, and D.J.Kosman (2000).
Spectroscopic analysis of the trinuclear cluster in the Fet3 protein from yeast, a multinuclear copper oxidase.
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10839819 U.Kües (2000).
Life history and developmental processes in the basidiomycete Coprinus cinereus.
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Myrothecium verrucaria bilirubin oxidase and its mutants for potential copper ligands.
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Molecular characterization of laccase genes from the basidiomycete Coprinus cinereus and heterologous expression of the laccase lcc1.
  Appl Environ Microbiol, 65, 4943-4948.  
10212209 F.Xu, A.E.Palmer, D.S.Yaver, R.M.Berka, G.A.Gambetta, S.H.Brown, and E.I.Solomon (1999).
Targeted mutations in a Trametes villosa laccase. Axial perturbations of the T1 copper.
  J Biol Chem, 274, 12372-12375.  
  10542175 G.Alexandre, R.Bally, B.L.Taylor, and I.B.Zhulin (1999).
Loss of cytochrome c oxidase activity and acquisition of resistance to quinone analogs in a laccase-positive variant of Azospirillum lipoferum.
  J Bacteriol, 181, 6730-6738.  
10551829 H.Huang, G.Zoppellaro, and T.Sakurai (1999).
Spectroscopic and kinetic studies on the oxygen-centered radical formed during the four-electron reduction process of dioxygen by Rhus vernicifera laccase.
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10583375 I.Gromov, A.Marchesini, O.Farver, I.Pecht, and D.Goldfarb (1999).
Azide binding to the trinuclear copper center in laccase and ascorbate oxidase.
  Eur J Biochem, 266, 820-830.  
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cDNA cloning of bilirubin oxidase from Pleurotus ostreatus strain Shinshu and its expression in Aspergillus sojae: an efficient screening of transformants, using the laccase activity of bilirubin oxidase.
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The reactions of copper proteins with nitric oxide.
  Biochim Biophys Acta, 1411, 310-322.  
  10543802 J.Zhao, and H.S.Kwan (1999).
Characterization, molecular cloning, and differential expression analysis of laccase genes from the edible mushroom Lentinula edodes.
  Appl Environ Microbiol, 65, 4908-4913.  
10226045 M.A.McGuirl, and D.M.Dooley (1999).
Copper-containing oxidases.
  Curr Opin Chem Biol, 3, 138-144.  
  10584012 M.Gelo-Pujic, H.H.Kim, N.G.Butlin, and G.T.Palmore (1999).
Electrochemical studies of a truncated laccase produced in Pichia pastoris.
  Appl Environ Microbiol, 65, 5515-5521.  
10473564 O.Farver, L.Bendahl, L.K.Skov, and I.Pecht (1999).
Human ceruloplasmin. Intramolecular electron transfer kinetics and equilibration.
  J Biol Chem, 274, 26135-26140.  
9649340 T.E.Machonkin, H.H.Zhang, B.Hedman, K.O.Hodgson, and E.I.Solomon (1998).
Spectroscopic and magnetic studies of human ceruloplasmin: identification of a redox-inactive reduced Type 1 copper site.
  Biochemistry, 37, 9570-9578.  
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