2ZWN

Crystal structure of the novel two-domain type laccase from a metagenome

• PDB DOI: https://doi.org/10.2210/pdb2ZWN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): metagenomes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-12-17 Released: 2009-04-07 
• Deposition Author(s): Komori, H., Miyazaki, K., Higuchi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.183 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

X-ray structure of a two-domain type laccase: a missing link in the evolution of multi-copper proteins

Komori, H., Miyazaki, K., Higuchi, Y.

(2009) FEBS Lett 583: 1189-1195

• PubMed: 19285076 
• DOI: https://doi.org/10.1016/j.febslet.2009.03.008
• Primary Citation of Related Structures:  
  2ZWN


• PubMed Abstract: 
  

  A multi-copper protein with two cupredoxin-like domains was identified from our in-house metagenomic database. The recombinant protein, mgLAC, contained four copper ions/subunits, oxidized various phenolic and non-phenolic substrates, and had spectroscopic properties similar to common laccases. X-ray structure analysis revealed a homotrimeric architecture for this enzyme, which resembles nitrite reductase (NIR). However, a difference in copper coordination was found at the domain interface. mgLAC contains a T2/T3 tri-nuclear copper cluster at this site, whereas a mononuclear T2 copper occupies this position in NIR. The trimer is thus an essential part of the architecture of two-domain multi-copper proteins, and mgLAC may be an evolutionary precursor of NIR.

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Organizational Affiliation: 

Department of Life Science, Graduate School of Life Science, University of Hyogo and Himeji Institute of Technology, Ako-gun, Hyogo 678-1297, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 115.43 kDa 
• Atom Count: 8,147 
• Modelled Residue Count: 949 
• Deposited Residue Count: 1,017 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
two-domain type laccase	A, B, C	339	metagenomes	Mutation(s): 0
UniProt
Find proteins for C0STU6 (uncultured bacterium) Explore C0STU6  Go to UniProtKB:  C0STU6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2O	E [auth A], F [auth A], K [auth B]	CU-O-CU LINKAGE Cu2 O BERDEBHAJNAUOM-UHFFFAOYSA-N
CU	D [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.183 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.669	α = 90
b = 100.945	β = 90
c = 124.106	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-07 
Deposition Author(s): Komori, H., Miyazaki, K., Higuchi, Y.

Revision History  

• Version 1.0: 2009-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations