Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase from Arabidopsis thaliana

Experimental Data Snapshot

  • Resolution: 3.06 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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Crystal Structure of the Chloroplastic Glutamine Phosphoribosylpyrophosphate Amidotransferase GPRAT2 FromArabidopsis thaliana.

Cao, X.Du, B.Han, F.Zhou, Y.Ren, J.Wang, W.Chen, Z.Zhang, Y.

(2020) Front Plant Sci 11: 157-157

  • DOI: https://doi.org/10.3389/fpls.2020.00157
  • Primary Citation of Related Structures:  

  • PubMed 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.

  • Organizational Affiliation

    Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amidophosphoribosyltransferase 2, chloroplastic
A, B
487Arabidopsis thalianaMutation(s): 0 
Gene Names: ASE2CIA1DOV1GPRAT2PURF2At4g34740T4L20.320
Find proteins for Q9STG9 (Arabidopsis thaliana)
Explore Q9STG9 
Go to UniProtKB:  Q9STG9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9STG9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.06 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.736α = 90
b = 179.736β = 90
c = 109.199γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Cootmodel building
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31670766

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description