Functional significance of serine 13 in the active site of glutathione S-transferase F3 from Oryza sativa

• Published in: Pesticide biochemistry and physiology Vol. 194; p. 105463
• Main Authors: Jin, Su-Bin, Jang, Si-Wook, Shin, Ji-Ae, Jung, Na-Hee, Kim, Hyun-A, Park, Seo-Young, Lee, Woo-Cheol, Kong, Kwang-Hoon
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.08.2023
• Subjects: 3-Dimensional structure; Active site; Binding Sites; Catalytic Domain; Glutathione - metabolism; Glutathione S-transferase; Glutathione Transferase - genetics; Glutathione Transferase - metabolism; Kinetics; Oryza - genetics; Oryza - metabolism; OsGSTF3; Serine; Serine residue; Site-directed mutagenesis; Sulfhydryl Compounds - metabolism; DNPG; 3-Dimensional structure; Active site; OsGSTF3; GST; CDNB; DCNB; CP; EPNP; SDS-PAGE; Site-directed mutagenesis; Serine residue; Glutathione S-transferase; GSH
• ISSN: 0048-3575; 1095-9939
• DOI: 10.1016/j.pestbp.2023.105463

Plant glutathione S-transferase (GST, EC 2.5.1.18) is an enzyme that detoxifies various electrophilic compounds including herbicides and organic pollutants by catalyzing the formation of conjugates with reduced glutathione (GSH). Although the structure and function of the GST subunits in rice, an important food in Asia, are not well understood, they are crucial for herbicide development. To investigate the role of active site residues in rice Phi-class GSTF3 (OsGSTF3), evolutionarily conserved serine residues were replaced with alanine using site-directed mutagenesis to obtain the mutants S13A, S38A, S69A, and S169A. These four mutants were expressed in Escherichia coli and purified to electrophoretic homogeneity using immobilized GSH affinity chromatography. Mutation of Ser13 to Ala resulted in substantial reductions in specific activities and kcat/Km values for the GSH-[1-chloro-2,4-dinitrobenzene (CDNB)] conjugation reaction. In contrast, mutations of Ser38, Ser69, and Ser169 to Ala had little effect on the activities and kinetic parameters. Additionally, the mutation of Ser13 to Ala significantly affected the KmGSH and I50 values of S-hexylglutathione and S-(2,4-dinitrophenyl)glutathione, which compete with GSH and the product of GSH-CDNB conjugation, respectively. A pH-log (kcat/KmCDNB) plot was used to estimate the pKa value of GSH in the enzyme-GSH complex of the wild-type enzyme, which was approximately 6.9. However, the pKa value of GSH in the enzyme-GSH complex of the S13A mutant was approximately 8.7, which was about 1.8 pK units higher than that of the wild-type enzyme. OsGSTF3 was also crystallized for crystallographic study, and the structure analyses revealed that Ser13 is located in the active site and that its side chain is in close proximity to the thiol group of glutathione bound in the enzyme. Based on these substitution effects on kinetic parameters, the dependence of kinetic parameters on the pH and 3-dimensional structure, it was suggested that Ser13 in rice OsGSTF3 is the residue responsible for catalytic activity by lowering the pKa of GSH in the enzyme-GSH complex and enhancing the nucleophilicity of the GSH thiol in the active site. Overall structure and active site of OsGSTF3 by X-ray crystal structure analysis. [Display omitted] •Crystal structure of rice glutathione S-transferase F3 in complex with glutathione.•Site-directed mutagenesis of evolutionarily conserved serine residues in OsGSTF3.•Functional significance of serine 13 in the catalytic mechanism of OsGSTF3.•Serine 13 of OsGSTF3 contributes to lower pKa and enhanced nucleophilicity of GSH thiol in active sites.