6J3H

Crystal structure of the glutathione S-transferase, CsGST83044, of Ceriporiopsis subvermispora in complex with glutathione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Identification of key residues for activities of atypical glutathione S-transferase of Ceriporiopsis subvermispora, a selective degrader of lignin in woody biomass, by crystallography and functional mutagenesis.

Osman, W.H.W.Mikami, B.Saka, N.Kondo, K.Lin, M.I.Nagata, T.Katahira, M.

(2019) Int.J.Biol.Macromol. 132: 222-229

  • DOI: 10.1016/j.ijbiomac.2019.03.199
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ceriporiopsis subvermispora (C. subvermispora) is a selective degrader of lignin in the woody biomass. Glutathione S-transferases (GSTs) are multifunctional enzymes that play important roles in cellular detoxification and metabolism. The crystal stru ...

    Ceriporiopsis subvermispora (C. subvermispora) is a selective degrader of lignin in the woody biomass. Glutathione S-transferases (GSTs) are multifunctional enzymes that play important roles in cellular detoxification and metabolism. The crystal structures of a GST of C. subvermispora, CsGST83044, in GSH-free and -bound forms were solved at 1.95 and 2.19 Å resolution, respectively. The structure of the GSH-bound form revealed that CsGST83044 can be categorized as an atypical-type of GST. In the GSH-bound form of CsGST83044, Asn22, Asn24, and Tyr46 are located closest to the sulfur atom and form hydrogen bonds with the thiol group. The functional mutagenesis indicated that they are critical for the enzymatic activities of CsGST83044. The critical residues of an atypical-type GST belonging to the GSTFuA class were revealed for the first time. A previous study indicated that CsGST83044 and another GST, CsGST63524, differ in substrate preference; CsGST83044 prefers smaller substrates than CsGST63524 for its esterase activity. The GSH-bound pocket of CsGST83044 turns out to be small, which may explain the preference for smaller substrates. Protein engineering of GSTs of C. subvermispora in the light of the obtained insight may pave a path in the future for utilization of the woody biomass.


    Organizational Affiliation

    Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan; Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutathione S-transferase
A, B, C, D
264Ceriporiopsis subvermispora (strain B)Mutation(s): 0 
Find proteins for M2QJS8 (Ceriporiopsis subvermispora (strain B))
Go to UniProtKB:  M2QJS8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GSH
Query on GSH

Download SDF File 
Download CCD File 
A, B, C, D
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 225.684α = 90.00
b = 48.397β = 129.27
c = 150.553γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data collection
SCALEPACKdata scaling
PHENIXrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan18H04550
Japan Society for the Promotion of ScienceJapan18K19397
Japan Society for the Promotion of ScienceJapan17K07307
Japan Society for the Promotion of ScienceJapan17H05878

Revision History 

  • Version 1.0: 2019-05-15
    Type: Initial release