4GXF | pdb_00004gxf

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: 2.73 Å
  • R-Value Free: 
    0.199 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4GXF

This is version 1.3 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: https://doi.org/10.1021/ja3088604
  • Primary Citation Related Structures: 
    4GXF, 4GY4

  • 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(XRD), spectroscopic (optical, EPR), and kinetics (stopped-flow) experiments on variants in which residue Tyr108 had been replaced by Phe or Ala through site-directed mutagenesis.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.

Macromolecule Content 

  • Total Structure Weight: 94.72 kDa 
  • Atom Count: 6,888 
  • Modeled Residue Count: 837 
  • Deposited Residue Count: 837 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative copper oxidase
A, B, C
279Streptomyces coelicolor A3(2)Mutation(s): 1 
Gene Names: SCO6712
UniProt
Find proteins for Q9XAL8 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9XAL8 
Go to UniProtKB:  Q9XAL8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XAL8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4

Query on PG4



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
G [auth A]
K [auth A]
L [auth A]
AA [auth C],
BA [auth C],
G [auth A],
K [auth A],
L [auth A],
O [auth B],
P [auth B],
S [auth B],
Y [auth C],
Z [auth C]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
H [auth A]
I [auth A]
D [auth A],
E [auth A],
F [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B],
Q [auth B],
T [auth C],
V [auth C],
W [auth C],
X [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
O

Query on O



Download:Ideal Coordinates CCD File
J [auth A],
R [auth B],
U [auth C]
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free:  0.199 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.66α = 90
b = 176.66β = 90
c = 176.85γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2012-11-07
    Changes: Database references
  • Version 1.2: 2013-07-10
    Changes: Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description