1V10 | pdb_00001v10

Structure of Rigidoporus lignosus laccase from hemihedrally twinned crystals


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.266 (Depositor) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

The Structure of Rigidoporus Lignosus Laccase Containing a Full Complement of Copper Ions, Reveals an Asymmetrical Arrangement for the T3 Copper Pair

Garavaglia, S.Cambria, M.T.Miglio, M.Ragusa, S.Iacobazzi, V.Palmieri, F.D'Ambrosio, C.Scaloni, A.Rizzi, M.

(2004) J Mol Biology 342: 1519

  • DOI: https://doi.org/10.1016/j.jmb.2004.07.100
  • Primary Citation Related Structures: 
    1V10

  • PubMed 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.


  • Organizational Affiliation
    • DiSCAFF-INFM, University of Piemonte Orientale A. Avogadro, 28100 Novara, Italy.

Macromolecule Content 

  • Total Structure Weight: 55.86 kDa 
  • Atom Count: 3,769 
  • Modeled Residue Count: 487 
  • Deposited Residue Count: 521 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LACCASE521Rigidoporus microporusMutation(s): 0 
EC: 1.10.3.2
UniProt
Find proteins for Q6H9H7 (Rigidoporus microporus)
Explore Q6H9H7 
Go to UniProtKB:  Q6H9H7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6H9H7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.266 (Depositor) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.914α = 90
b = 124.914β = 90
c = 95.117γ = 120
Software Package:
Software NamePurpose
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary