3TA4

Small laccase from Amycolatopsis sp. ATCC 39116 complexed with 1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)-1,3-dihydroxypropane


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


This is version 1.5 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 oxidaseA [auth F],
B [auth D],
C [auth E]
299Amycolatopsis sp. ATCC 39116Mutation(s): 0 
EC: 1.10.3.2
UniProt
Find proteins for J9PBQ8 (Amycolatopsis sp. (strain ATCC 39116 / 75iv2))
Explore J9PBQ8 
Go to UniProtKB:  J9PBQ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ9PBQ8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TO2
Query on TO2

Download Ideal Coordinates CCD File 
J [auth F](1R,2S)-1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol
C18 H22 O6
IEWUCQVFAWBYOC-ZWKOTPCHSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
D [auth F]
E [auth F]
F
G [auth F]
H [auth F]
D [auth F],
E [auth F],
F,
G [auth F],
H [auth F],
I [auth F],
K [auth D],
L [auth D],
M [auth D],
N [auth D],
O [auth D],
P [auth D],
Q [auth E],
R [auth E],
S [auth E],
T [auth E]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.42α = 90
b = 115.26β = 90
c = 163.51γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2014-06-11
    Changes: Database references
  • Version 1.2: 2014-10-01
    Changes: Database references
  • Version 1.3: 2017-10-11
    Changes: Data collection
  • Version 1.4: 2017-10-25
    Changes: Author supporting evidence
  • Version 1.5: 2024-02-28
    Changes: Data collection, Database references, Derived calculations