Crystal Structure of the Chloroplastic Glutamine Phosphoribosylpyrophosphate Amidotransferase GPRAT2 From Arabidopsis thaliana

Xueli Cao; Bowen Du; Fengjiao Han; Yu Zhou; Junhui Ren; Wenhe Wang; Zeliang Chen; Yi Zhang

doi:10.3389/fpls.2020.00157

Crystal Structure of the Chloroplastic Glutamine Phosphoribosylpyrophosphate Amidotransferase GPRAT2 From Arabidopsis thaliana

Front Plant Sci. 2020 Feb 27:11:157. doi: 10.3389/fpls.2020.00157. eCollection 2020.

Authors

Xueli Cao¹, Bowen Du¹, Fengjiao Han¹, Yu Zhou², Junhui Ren¹, Wenhe Wang¹, Zeliang Chen^{1

3}, Yi Zhang¹

Affiliations

¹ Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, China.
² Department of Computational Chemistry, National Institute of Biological Sciences, Beijing, China.
³ Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.

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.

Keywords: Arabidopsis thaliana; DAS734; X-ray crystallography; chloroplastic glutamine phosphoribosylpyrophosphate amidotransferase; competitive inhibition; herbicide.