3TAS

Small laccase from Streptomyces viridosporus T7A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Roles of small laccases from Streptomyces in lignin degradation.

Majumdar, S.Lukk, T.Solbiati, J.O.Bauer, S.Nair, S.K.Cronan, J.E.Gerlt, J.A.

(2014) Biochemistry 53: 4047-4058

  • DOI: https://doi.org/10.1021/bi500285t
  • Primary Citation of Related Structures:  
    3T9W, 3TA4, 3TAS, 3TBB, 3TBC

  • PubMed Abstract: 

    Laccases (EC 1.10.3.2) are multicopper oxidases that can oxidize a range of substrates, including phenols, aromatic amines, and nonphenolic substrates. To investigate the involvement of the small Streptomyces laccases in lignin degradation, we generated acid-precipitable polymeric lignin obtained in the presence of wild-type Streptomyces coelicolor A3(2) (SCWT) and its laccase-less mutant (SCΔLAC) in the presence of Miscanthus x giganteus lignocellulose. The results showed that strain SCΔLAC was inefficient in degrading lignin compared to strain SCWT, thereby supporting the importance of laccase for lignin degradation by S. coelicolor A3(2). We also studied the lignin degradation activity of laccases from S. coelicolor A3(2), Streptomyces lividans TK24, Streptomyces viridosporus T7A, and Amycolatopsis sp. 75iv2 using both lignin model compounds and ethanosolv lignin. All four laccases degraded a phenolic model compound (LM-OH) but were able to oxidize a nonphenolic model compound only in the presence of redox mediators. Their activities are highest at pH 8.0 with a low krel/Kapp for LM-OH, suggesting that the enzymes’ natural substrates must be different in shape or chemical nature. Crystal structures of the laccases from S. viridosporus T7A (SVLAC) and Amycolatopsis sp. 75iv2 were determined both with and without bound substrate. This is the first report of a crystal structure for any laccase bound to a nonphenolic β-O-4 lignin model compound. An additional zinc metal binding site in SVLAC was also identified. The ability to oxidize and/or rearrange ethanosolv lignin provides further evidence of the utility of laccase activity for lignin degradation and/or modification.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Small laccase, multi-copper oxidase
A, B, C
313Streptomyces viridosporusMutation(s): 0 
EC: 1.10.3.2
UniProt
Find proteins for J9PBR2 (Streptomyces viridosporus)
Explore J9PBR2 
Go to UniProtKB:  J9PBR2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ9PBR2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
L [auth A],
LA [auth C],
M [auth A],
X [auth B],
Y [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
MA [auth C]
N [auth A]
NA [auth C]
AA [auth B],
BA [auth B],
MA [auth C],
N [auth A],
NA [auth C],
O [auth A],
Z [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
IA [auth C],
J [auth A],
W [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
EA [auth C]
F [auth A]
FA [auth C]
D [auth A],
E [auth A],
EA [auth C],
F [auth A],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
CA [auth B]
DA [auth B]
OA [auth C]
P [auth A]
PA [auth C]
CA [auth B],
DA [auth B],
OA [auth C],
P [auth A],
PA [auth C],
Q [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
OXY
Query on OXY

Download Ideal Coordinates CCD File 
JA [auth C],
K [auth A],
KA [auth C]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.3α = 90
b = 157.18β = 90
c = 162.33γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2014-06-11
    Changes: Database references
  • Version 1.2: 2014-10-01
    Changes: Database references
  • Version 1.3: 2017-10-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description