4M3H

Crystal structure of small laccase Ssl1 from Streptomyces sviceus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and redox properties of the small laccase Ssl1 from Streptomyces sviceus.

Gunne, M.Hoppner, A.Hagedoorn, P.L.Urlacher, V.B.

(2014) FEBS J 281: 4307-4318

  • DOI: https://doi.org/10.1111/febs.12755
  • Primary Citation of Related Structures:  
    4M3H

  • PubMed Abstract: 

    Laccases (EC 1.10.3.2) are members of the multicopper oxidase family. They oxidize diverse electron-rich substrates through electron abstraction by the type 1 copper ion in the enzyme active site. Abstracted electrons are transferred to the trinuclear copper cluster, where molecular oxygen serves as final acceptor and is reduced to water. Laccase activity is assumed to depend on the redox potential of its type 1 copper ion. Whereas numerous studies have been undertaken to elucidate the determinants of the redox potential of type 1 copper ions in one-domain cupredoxins and in three-domain laccases, such experimental investigations are lacking for recently described, small, two-domain laccases. In this work, the crystal structure of the small laccase Ssl1 from Streptomyces sviceus was solved, and the positions that might influence the redox potential of Ssl1 were depicted. On the basis of this knowledge, several Ssl1 variants were constructed with an increase in redox potential of 16-81 mV, from 375 mV to 391-456 mV. Mutation of residues in close proximity to the type 1 copper center resulted in a predicted increase in the redox potential of the copper center; however, there was a reduced specific activity for the oxidation of 2,6-dimethoxyphenol, which has a relatively low redox potential. Mutations more distant to the type 1 copper also led to an increased redox potential of the copper center, and resulted in variants able to oxidize the high redox potential substrates 1,2-dihydroxyanthraquinone-3-sulfonic acid (Alizarin Red S) and indigo carmine more efficiently than wild-type Ssl1.


  • Organizational Affiliation

    Institute of Biochemistry, Heinrich-Heine-Universität Düsseldorf, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Copper oxidase
A, B, C
325Streptomyces sviceusMutation(s): 0 
Gene Names: SSEG_02446
EC: 1.10.3.2
UniProt
Find proteins for B5HSR1 (Streptomyces sviceus (strain ATCC 29083 / DSM 924 / JCM 4929 / NBRC 13980 / NCIMB 11184 / NRRL 5439 / UC 5370))
Explore B5HSR1 
Go to UniProtKB:  B5HSR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5HSR1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
P [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
O
Query on O

Download Ideal Coordinates CCD File 
J [auth B],
M [auth B]
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.54α = 90
b = 103.82β = 90
c = 162.26γ = 90
Software Package:
Software NamePurpose
EDNAdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description