4GY4

Role of the biradical intermediate observed during the turnover of SLAC: A two-domain laccase from Streptomyces coelicolor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Involvement of Tyr108 in the enzyme mechanism of the small laccase from Streptomyces coelicolor

Gupta, A.Nederlof, I.Sottini, S.Tepper, A.W.Groenen, E.J.Thomassen, E.A.Canters, G.W.

(2012) J.Am.Chem.Soc. 134: 18213-18216

  • DOI: 10.1021/ja3088604
  • Primary Citation of Related Structures:  4GXF

  • PubMed Abstract: 
  • The enzyme mechanism of the multicopper oxidase (MCO) SLAC from Streptomyces coelicolor was investigated by structural (XRD), spectroscopic (optical, EPR), and kinetics (stopped-flow) experiments on variants in which residue Tyr108 had been replaced ...

    The enzyme mechanism of the multicopper oxidase (MCO) SLAC from Streptomyces coelicolor was investigated by structural (XRD), spectroscopic (optical, EPR), and kinetics (stopped-flow) experiments on variants in which residue Tyr108 had been replaced by Phe or Ala through site-directed mutagenesis. Contrary to the more common three-domain MCOs, a tyrosine in the two-domain SLAC is found to participate in the enzyme mechanism by providing an electron during oxygen reduction, giving rise to the temporary appearance of a tyrosyl radical. The relatively low k(cat)/K(M) of SLAC and the involvement of Y108 in the enzyme mechanism may reflect an adaptation to a milieu in which there is an imbalance between the available reducing and oxidizing co-substrates. The purported evolutionary relationship between the two-domain MCOs and human ceruloplasmin appears to extend not only to the 3D structure and the mode of binding of the Cu's in the trinuclear center, as noted before, but also to the enzyme mechanism.


    Organizational Affiliation

    Leiden Institute of Physics, Leiden University, Leiden, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative copper oxidase
A, B, C
278Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)N/A
Find proteins for Q9XAL8 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Go to UniProtKB:  Q9XAL8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O
Query on O

Download SDF File 
Download CCD File 
A, B, C
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A, B, C
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B, C
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.215 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 178.440α = 90.00
b = 178.440β = 90.00
c = 177.770γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2012-11-07
    Type: Database references
  • Version 1.2: 2013-07-10
    Type: Database references