2ZWN | pdb_00002zwn

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.183 (Depositor), 0.189 (DCC)
R-Value Work:
0.159 (Depositor), 0.166 (DCC)
R-Value Observed:
0.161 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2009.03.008
Primary Citation 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.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

| 3D Structure

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 A0ACD6B9B7 (uncultured bacterium) Explore A0ACD6B9B7 Go to UniProtKB: A0ACD6B9B7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B9B7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C2O Query on C2O Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B]	E [auth A], F [auth A], K [auth B]	CU-O-CU LINKAGE Cu₂ O BERDEBHAJNAUOM-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] MOL2 format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] mmCIF format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C]	D [auth A] G [auth A] I [auth B] J [auth B] L [auth C] 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		Interactions Focus chain D [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.183 (Depositor), 0.189 (DCC)
R-Value Work: 0.159 (Depositor), 0.166 (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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-04-07

Deposition Author(s):

Komori, H.

Miyazaki, K.

Higuchi, Y.

Revision History (Full details and data files)

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