S-formylglutathione hydrolase from Variovorax sp. PAMC 28711

Experimental Data Snapshot

  • Resolution: 2.38 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

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Structural basis for the substrate specificity of an S-formylglutathione hydrolase derived from Variovorax sp. PAMC 28711.

Hwang, J.Kim, B.Lee, M.J.Nam, Y.Youn, U.J.Lee, C.S.Oh, T.J.Park, H.H.Do, H.Lee, J.H.

(2022) Biochem Biophys Res Commun 629: 159-164

  • DOI: https://doi.org/10.1016/j.bbrc.2022.09.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    S-Formylglutathione hydrolase was originally known to catalyze the hydrolysis of S-formylglutathione to formate and glutathione. However, this enzyme has a broader esterase activity toward substrates containing thioester and ester bonds. In a previous study, we identified a new S-formylglutathione hydrolase (VaSFGH) gene in the Antarctic bacterium Variovorax sp. PAMC 28711, and recombinant VaSFGH protein was purified and characterized. Previous enzyme activity assays showed that VaSFGH has high activity, especially toward short-chain p-nitrophenyl esters (C2-C4). In this study, we determined the crystal structure of substrate-free VaSFGH at a resolution of 2.38 Å. In addition, p-nitrophenyl ester-bound VaSFGH structure models were generated by molecular docking simulations to obtain structural evidence of its substrate specificity. Comparative structural analysis of the apo-form and p-nitrophenyl ester-bound VaSFGH model structures revealed that large substrates could not bind inside the hydrophobic substrate-binding pocket because of the intrinsically static and relatively small substrate-binding pocket size of VaSFGH. This study provides useful information for further protein engineering of SFGHs for industrial use.

  • Organizational Affiliation

    Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-formylglutathione hydrolase
A, B, C
295Variovorax sp.Mutation(s): 0 
Gene Names: AX767_16275
Find proteins for A0A126ZFJ3 (Variovorax sp. PAMC 28711)
Explore A0A126ZFJ3 
Go to UniProtKB:  A0A126ZFJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A126ZFJ3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.38 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.204α = 90
b = 76.437β = 91.192
c = 199.865γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfPM22030

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description