4XT0

Crystal Structure of Beta-etherase LigF from Sphingobium sp. strain SYK-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of beta-Aryl Ether Bonds in Lignin.

Helmich, K.E.Pereira, J.H.Gall, D.L.Heins, R.A.McAndrew, R.P.Bingman, C.Deng, K.Holland, K.C.Noguera, D.R.Simmons, B.A.Sale, K.L.Ralph, J.Donohue, T.J.Adams, P.D.Phillips, G.N.

(2016) J.Biol.Chem. 291: 5234-5246

  • DOI: 10.1074/jbc.M115.694307
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles t ...

    Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, we present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50-70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.


    Organizational Affiliation

    From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein LigF
A
246Sphingobium sp. (strain NBRC 103272 / SYK-6)Mutation(s): 0 
Gene Names: ligF
Find proteins for G2IN92 (Sphingobium sp. (strain NBRC 103272 / SYK-6))
Go to UniProtKB:  G2IN92
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GSH
Query on GSH

Download SDF File 
Download CCD File 
A
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
A
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.158 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 123.708α = 90.00
b = 123.708β = 90.00
c = 66.416γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
HKL-2000data scaling
Cootmodel building
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (United States)United StatesDE-FC02-07ER64494

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-03-16
    Type: Database references, Source and taxonomy
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Derived calculations
  • Version 1.3: 2017-11-22
    Type: Refinement description