8ET5 | pdb_00008et5

Crystal structure of arabidopsis thaliana acetohydroxyacid synthase S653T mutant in complex with amidosulfuron


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 
    0.217 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the Commercial Herbicide, Amidosulfuron, in Complex with Arabidopsis thaliana Acetohydroxyacid Synthase.

Cheng, Y.Lonhienne, T.Garcia, M.D.Williams, C.M.Schenk, G.Guddat, L.W.

(2023) J Agric Food Chem 71: 5117-5126

  • DOI: https://doi.org/10.1021/acs.jafc.2c08528
  • Primary Citation Related Structures: 
    8ET4, 8ET5

  • PubMed Abstract: 

    Amidosulfuron (AS) is from the commercial sulfonylurea herbicide family. It is highly effective against dicot broad-leaf weeds. This herbicide targets acetohydroxyacid synthase (AHAS), the first enzyme in the branched chain amino acid biosynthesis pathway. Here, we have determined the crystal structure of AS in complex with wildtype Arabidopsis thaliana AHAS ( At AHAS) and with the resistance mutant, S653T. In both structures, the cofactor, ThDP, is modified to a peracetate adduct, consistent with time-dependent accumulative inhibition. Compared to other AHAS-inhibiting herbicides of the sulfonylurea family, AS lacks a second aromatic ring. The replacement is an aryl sulfonyl group with a reduced number of interactions with the enzyme and relatively low affinity ( K i = 4.2 μM vs low nM when two heteroaromatic rings are present). This study shows that effective herbicides can have a relatively high K i for plant AHAS but can still be a potent herbicide provided accumulative inhibition also occurs.


  • Organizational Affiliation
    • School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia.

Macromolecule Content 

  • Total Structure Weight: 67.08 kDa 
  • Atom Count: 4,623 
  • Modeled Residue Count: 582 
  • Deposited Residue Count: 590 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetolactate synthase, chloroplastic590Arabidopsis thalianaMutation(s): 1 
Gene Names: ALSAHASCSR1TZP5At3g48560T8P19.70
EC: 2.2.1.6
UniProt
Find proteins for P17597 (Arabidopsis thaliana)
Explore P17597 
Go to UniProtKB:  P17597
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17597
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
C [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
AUJ

Query on AUJ



Download:Ideal Coordinates CCD File
F [auth A]2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-[(1~{S})-1-(dioxidanyl)-1-oxidanyl-ethyl]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate
C14 H23 N4 O10 P2 S
IMARWCCDLODQKU-AWEZNQCLSA-N
WRQ

Query on WRQ



Download:Ideal Coordinates CCD File
D [auth A]N-{[(4,6-dimethoxypyrimidin-2-yl)carbamoyl]sulfamoyl}-N-methylmethanesulfonamide
C9 H15 N5 O7 S2
CTTHWASMBLQOFR-UHFFFAOYSA-N
NHE

Query on NHE



Download:Ideal Coordinates CCD File
E [auth A]2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
TLA

Query on TLA



Download:Ideal Coordinates CCD File
G [auth A]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
L [auth A],
M [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG

Query on MG



Download:Ideal Coordinates CCD File
B [auth A],
H [auth A],
I [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.593α = 90
b = 179.593β = 90
c = 184.772γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary