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Cao X, Du B, Han F, Zhou Y, Ren J, Wang W, Chen Z, Zhang Y. Crystal Structure of the Chloroplastic Glutamine Phosphoribosylpyrophosphate Amidotransferase GPRAT2 From Arabidopsis thaliana. Front Plant Sci 2020; 11:157. [PMID: 32174940 PMCID: PMC7056826 DOI: 10.3389/fpls.2020.00157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/31/2020] [Indexed: 05/03/2023]
Abstract
Chloroplastic glutamine phosphoribosylpyrophosphate amidotransferase (GPRATase) catalyzes the first committed step of de novo purine biosynthesis in Arabidopsis thaliana, and DAS734 is a direct and specific inhibitor of AtGPRAT, with phytotoxic effects similar to the leaf beaching phenotypes of known AtGPRAT genetic mutants, especially cia1 and atd2. However, the structure of AtGPRAT and the inhibition mode of DAS734 still remain poorly understood. In this study, we solved the structure of AtGPRAT2, which revealed structural differences between AtGPRAT2 and bacterial enzymes. Kinetics assay demonstrated that DAS734 behaves as a competitive inhibitor for the substrate phosphoribosyl pyrophosphate (PRPP) of AtGPRAT2. Docking studies showed that DAS734 forms electrostatic interactions with R264 and hydrophobic interactions with several residues, which was verified by binding assays. Collectively, our study provides important insights into the inhibition mechanism of DAS734 to AtGPRAT2 and sheds light on future studies into further development of more potent herbicides targeting Arabidopsis GPRATases.
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Affiliation(s)
- Xueli Cao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, China
| | - Bowen Du
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, China
| | - Fengjiao Han
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, China
| | - Yu Zhou
- Department of Computational Chemistry, National Institute of Biological Sciences, Beijing, China
| | - Junhui Ren
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, China
| | - Wenhe Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, China
| | - Zeliang Chen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, China
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yi Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, China
- *Correspondence: Yi Zhang,
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