1A65

TYPE-2 CU-DEPLETED LACCASE FROM COPRINUS CINEREUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.160 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of the type-2 Cu depleted laccase from Coprinus cinereus at 2.2 A resolution.

Ducros, V.Brzozowski, A.M.Wilson, K.S.Brown, S.H.Ostergaard, P.Schneider, P.Yaver, D.S.Pedersen, A.H.Davies, G.J.

(1998) Nat Struct Biol 5: 310-316

  • DOI: https://doi.org/10.1038/nsb0498-310
  • Primary Citation of Related Structures:  
    1A65

  • PubMed 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.


  • Organizational Affiliation

    Department of Chemistry, University of York, Heslington, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LACCASE504Coprinopsis cinereaMutation(s): 0 
EC: 1.10.3.2
UniProt
Find proteins for Q9Y780 (Coprinopsis cinerea)
Explore Q9Y780 
Go to UniProtKB:  Q9Y780
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y780
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PYE
Query on PYE

Download Ideal Coordinates CCD File 
C [auth A]TETRAHYDROPYRAN
C5 H10 O
DHXVGJBLRPWPCS-UHFFFAOYSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
O
Query on O

Download Ideal Coordinates CCD File 
G [auth A]OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.39α = 90
b = 85.72β = 90
c = 143.07γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-03-30
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-08-02
    Changes: Database references, Refinement description, Structure summary