6LBP

Structure of the Glutamine Phosphoribosylpyrophosphate Amidotransferase from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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:  
    6LBP

  • 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

    Department of Computational Chemistry, National Institute of Biological Sciences, Beijing, China.


Macromolecules
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
EC: 2.4.2.14
UniProt
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
PDB_EXTRACTdata extraction
Cootmodel building
SCALEPACKdata scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



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