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PDBsum entry 1v10
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protein metals links
Oxidase PDB id
1v10

 

 

 

 

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Contents
Protein chain
487 a.a. *
Metals
_CU ×4
Waters ×81
* Residue conservation analysis
PDB id:
1v10
Name: Oxidase
Title: Structure of rigidoporus lignosus laccase from hemihedrally twinned crystals
Structure: Laccase. Chain: a. Ec: 1.10.3.2
Source: Rigidoporus lignosus. Organism_taxid: 219653. Atcc: aj609490
Resolution:
1.70Å     R-factor:   0.226     R-free:   0.266
Authors: M.Rizzi,S.Garavaglia,F.Palmieri,A.Cambria
Key ref:
S.Garavaglia et al. (2004). The structure of Rigidoporus lignosus Laccase containing a full complement of copper ions, reveals an asymmetrical arrangement for the T3 copper pair. J Mol Biol, 342, 1519-1531. PubMed id: 15364578 DOI: 10.1016/j.jmb.2004.07.100
Date:
02-Apr-04     Release date:   16-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q6H9H7  (Q6H9H7_9APHY) -  Laccase from Rigidoporus microporus
Seq:
Struc: 		 
Seq:
Struc: 		521 a.a.
487 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 hydroquinone + O2 = 4 benzosemiquinone + 2 H2O
4 × hydroquinone
 + O2
 = 4 × benzosemiquinone
 + 2 × H2O
      Cofactor: Cu cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Key reference    
 
 
DOI no: 10.1016/j.jmb.2004.07.100 J Mol Biol 342:1519-1531 (2004)
PubMed id: 15364578  
 
 
The structure of Rigidoporus lignosus Laccase containing a full complement of copper ions, reveals an asymmetrical arrangement for the T3 copper pair.
S.Garavaglia, M.T.Cambria, M.Miglio, S.Ragusa, V.Iacobazzi, F.Palmieri, C.D'Ambrosio, A.Scaloni, M.Rizzi.
 
  ABSTRACT  
 
Laccase is a multicopper blue oxidase that couples the four-electron reduction of oxygen with the oxidation of a broad range of organic substrates, including phenols and arylamines. The enzyme is the object of intense biotechnological research, due to its employment in bioremediation of soils and water as well as in other biotechnological applications. We report here the cDNA and protein sequences, the post-translational modifications, the crystallization and X-ray structure determination of a laccase from the white-rot fungus Rigidoporus lignosus. The amino acid residues sequence deduced from cDNA clearly identified a pre-sequence of 21 residues representing the signal for extra-cellular localization. Mass spectrometry analysis performed on the salvage enzyme, confirmed the deduced sequence and precisely mapped two glycosylation sites at Asn337 and Asn435, determining the nature of the bound glycosidic moieties. The crystal structure was determined at 1.7A resolution from perfectly hemihedrally twinned crystals, by molecular replacement technique. While the overall structure closely resembled those reported for other fungal laccases, the analysis of the T2/T3 trinuclear cluster revealed an unprecedented coordination sphere for the T3 copper pair. No bridging oxygen ligand was present between the two T3 copper ions, which were no longer symmetrically coordinated. The observed structure could represent an intermediate along the process of four-electron reduction of oxygen to water taking place at the trinuclear copper cluster.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Representation of the T1 and T2/T3 copper centers in RlLa. (A) Schematic representation of the T1 (Cu1) copper center, reporting inter-atomic distances between relevant atoms. (B) Stereo view around the T1 center; residues and copper ion are represented as ball-and-stick and sphere, respectively. (C) Schematic representation of the T2/T3 tri- nuclear copper center, reporting inter-atomic distances between relevant atoms. (D) Stereo view for the T2/T3 copper ions (Cu2, Cu3b and Cu3a) and their coordinating residues; copper ions and water molecules are depicted as green and red spheres, respectively. Amino acid residues are drawn as ball-and-stick. Panel (B) and (C) were generated using MOLSCRIPT. 51 		Figure 6.
Figure 6. Stereo view around the T2/T3 center showing the electron density of the Fo-F c difference Fourier omit map (contouring level is 4 sigma). Water molecules and copper atoms are depicted as red and green sphere, respectively. The figure was generated using BOBSCRIPT. 52
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 342, 1519-1531) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20711819 M.T.Cambria, S.Ragusa, V.Calabrese, and A.Cambria (2011).
Enhanced Laccase Production in White-Rot Fungus Rigidoporus lignosus by the Addition of Selected Phenolic and Aromatic Compounds.
  Appl Biochem Biotechnol, 163, 415-422.  
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.
  Anal Bioanal Chem, 399, 361-366.  
20175122 T.K.Lundell, M.R.Mäkelä, and K.Hildén (2010).
Lignin-modifying enzymes in filamentous basidiomycetes--ecological, functional and phylogenetic review.
  J Basic Microbiol, 50, 5.  
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.
  Dalton Trans, 39, 2875-2882.
PDB codes: 4ako 4akp 4akq
19034452 C.Pezzella, F.Autore, P.Giardina, A.Piscitelli, G.Sannia, and V.Faraco (2009).
The Pleurotus ostreatus laccase multi-gene family: isolation and heterologous expression of new family members.
  Curr Genet, 55, 45-57.  
18581264 D.W.Wong (2009).
Structure and action mechanism of ligninolytic enzymes.
  Appl Biochem Biotechnol, 157, 174-209.  
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.
  Proc Natl Acad Sci U S A, 106, 6585-6590.  
19360388 K.Hildén, T.K.Hakala, and T.Lundell (2009).
Thermotolerant and thermostable laccases.
  Biotechnol Lett, 31, 1117-1128.  
19297322 K.Kataoka, R.Sugiyama, S.Hirota, M.Inoue, K.Urata, Y.Minagawa, D.Seo, and T.Sakurai (2009).
Four-electron Reduction of Dioxygen by a Multicopper Oxidase, CueO, and Roles of Asp112 and Glu506 Located Adjacent to the Trinuclear Copper Center.
  J Biol Chem, 284, 14405-14413.  
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
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.
  J Biol Chem, 284, 10174-10180.
PDB code: 3g5w
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.  
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.
  Org Biomol Chem, 6, 868-878.  
18350382 M.T.Cambria, Z.Minniti, V.Librando, and A.Cambria (2008).
Degradation of polycyclic aromatic hydrocarbons by Rigidoporus lignosus and its laccase in the presence of redox mediators.
  Appl Biochem Biotechnol, 149, 1-8.  
17242517 I.Bento, C.Peixoto, V.N.Zaitsev, and P.F.Lindley (2007).
Ceruloplasmin revisited: structural and functional roles of various metal cation-binding sites.
  Acta Crystallogr D Biol Crystallogr, 63, 240-248.
PDB code: 2j5w
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.
  J Am Chem Soc, 129, 13127-13136.  
17897461 M.Ferraroni, N.M.Myasoedova, V.Schmatchenko, A.A.Leontievsky, L.A.Golovleva, A.Scozzafava, and F.Briganti (2007).
Crystal structure of a blue laccase from Lentinus tigrinus: evidences for intermediates in the molecular oxygen reductive splitting by multicopper oxidases.
  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.
  Biochemistry (Mosc), 72, 1136-1150.  
16317711 A.Marjasvaara, K.Kruus, and P.Vainiotalo (2006).
A laccase study by electrospray ionization Fourier transform ion cyclotron resonance MS: copper depletion, glycoforms and stability.
  J Mass Spectrom, 41, 91-97.  
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.  
16568314 K.Murugesan, M.Arulmani, I.H.Nam, Y.M.Kim, Y.S.Chang, and P.T.Kalaichelvan (2006).
Purification and characterization of laccase produced by a white rot fungus Pleurotus sajor-caju under submerged culture condition and its potential in decolorization of azo dyes.
  Appl Microbiol Biotechnol, 72, 939-946.  
16472305 P.Baldrian (2006).
Fungal laccases - occurrence and properties.
  FEMS Microbiol Rev, 30, 215-242.  
16680453 P.Durão, I.Bento, A.T.Fernandes, E.P.Melo, P.F.Lindley, and L.O.Martins (2006).
Perturbations of the T1 copper site in the CotA laccase from Bacillus subtilis: structural, biochemical, enzymatic and stability studies.
  J Biol Inorg Chem, 11, 514-526.  
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, (), 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.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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