4E9V

Multicopper Oxidase mgLAC (data1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

New insights into the catalytic active-site structure of multicopper oxidases.

Komori, H.Sugiyama, R.Kataoka, K.Miyazaki, K.Higuchi, Y.Sakurai, T.

(2014) Acta Crystallogr D Biol Crystallogr 70: 772-779

  • DOI: https://doi.org/10.1107/S1399004713033051
  • Primary Citation of Related Structures:  
    4E9V, 4E9W, 4E9X, 4E9Y, 4NER

  • PubMed Abstract: 

    Structural models determined by X-ray crystallography play a central role in understanding the catalytic mechanism of enzymes. However, X-ray radiation generates hydrated electrons that can cause significant damage to the active sites of metalloenzymes. In the present study, crystal structures of the multicopper oxidases (MCOs) CueO from Escherichia coli and laccase from a metagenome were determined. Diffraction data were obtained from a single crystal under low to high X-ray dose conditions. At low levels of X-ray exposure, unambiguous electron density for an O atom was observed inside the trinuclear copper centre (TNC) in both MCOs. The gradual reduction of copper by hydrated electrons monitored by measurement of the Cu K-edge X-ray absorption spectra led to the disappearance of the electron density for the O atom. In addition, the size of the copper triangle was enlarged by a two-step shift in the location of the type III coppers owing to reduction. Further, binding of O2 to the TNC after its full reduction was observed in the case of the laccase. Based on these novel structural findings, the diverse resting structures of the MCOs and their four-electron O2-reduction process are discussed.


  • Organizational Affiliation

    Faculty of Education, Kagawa University, 1-1 Saiwai-cho, Takamatsu, Kagawa 760-8522, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multicopper oxidase
A, B, C
339uncultured bacteriumMutation(s): 0 
Gene Names: mco
UniProt
Find proteins for C0STU6 (uncultured bacterium)
Explore C0STU6 
Go to UniProtKB:  C0STU6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC0STU6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
G [auth A]
H [auth A]
K [auth B]
D [auth A],
E [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
N [auth B],
O [auth B],
Q [auth C],
R [auth C],
T [auth C],
U [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
OH
Query on OH

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B],
S [auth C]
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
O
Query on O

Download Ideal Coordinates CCD File 
F [auth A],
P [auth B],
V [auth C]
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.728α = 90
b = 101.13β = 90
c = 123.959γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Database references