5WKC

Saccharomyces cerevisiae acetohydroxyacid synthase in complex with the herbicide penoxsulam


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural insights into the mechanism of inhibition of AHAS by herbicides.

Lonhienne, T.Garcia, M.D.Pierens, G.Mobli, M.Nouwens, A.Guddat, L.W.

(2018) Proc Natl Acad Sci U S A 115: E1945-E1954

  • DOI: https://doi.org/10.1073/pnas.1714392115
  • Primary Citation of Related Structures:  
    5WJ1, 5WKC

  • PubMed Abstract: 

    Acetohydroxyacid synthase (AHAS), the first enzyme in the branched amino acid biosynthesis pathway, is present only in plants and microorganisms, and it is the target of >50 commercial herbicides. Penoxsulam (PS), which is a highly effective broad-spectrum AHAS-inhibiting herbicide, is used extensively to control weed growth in rice crops. However, the molecular basis for its inhibition of AHAS is poorly understood. This is despite the availability of structural data for all other classes of AHAS-inhibiting herbicides. Here, crystallographic data for Saccharomyces cerevisiae AHAS (2.3 Å) and Arabidopsis thaliana AHAS (2.5 Å) in complex with PS reveal the extraordinary molecular mechanisms that underpin its inhibitory activity. The structures show that inhibition of AHAS by PS triggers expulsion of two molecules of oxygen bound in the active site, releasing them as substrates for an oxygenase side reaction of the enzyme. The structures also show that PS either stabilizes the thiamin diphosphate (ThDP)-peracetate adduct, a product of this oxygenase reaction, or traps within the active site an intact molecule of peracetate in the presence of a degraded form of ThDP: thiamine aminoethenethiol diphosphate. Kinetic analysis shows that PS inhibits AHAS by a combination of events involving FAD oxidation and chemical alteration of ThDP. With the emergence of increasing levels of resistance toward front-line herbicides and the need to optimize the use of arable land, these data suggest strategies for next generation herbicide design.


  • Organizational Affiliation

    School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; [email protected] [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetolactate synthase catalytic subunit, mitochondrialA,
B,
C [auth E]
677Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ILV2SMR1YMR108WYM9718.07
EC: 2.2.1.6
UniProt
Find proteins for P07342 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07342 
Go to UniProtKB:  P07342
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07342
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Acetolactate synthase catalytic subunit, mitochondrial677Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ILV2SMR1YMR108WYM9718.07
EC: 2.2.1.6
UniProt
Find proteins for P07342 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07342 
Go to UniProtKB:  P07342
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07342
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
Q [auth E],
V [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
AUJ
Query on AUJ

Download Ideal Coordinates CCD File 
I [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
PXD
Query on PXD

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
P [auth E],
U [auth D]
2-(2,2-difluoroethoxy)-N-(5,8-dimethoxy[1,2,4]triazolo[1,5-c]pyrimidin-2-yl)-6-(trifluoromethyl)benzenesulfonamide
C16 H14 F5 N5 O5 S
SYJGKVOENHZYMQ-UHFFFAOYSA-N
TP9
Query on TP9

Download Ideal Coordinates CCD File 
M [auth B],
R [auth E],
W [auth D]
(3Z)-4-{[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]AMINO}-3-MERCAPTOPENT-3-EN-1-YL TRIHYDROGEN DIPHOSPHATE
C11 H18 N4 O7 P2 S
WTQDUFKDQLXDPH-YFHOEESVSA-L
F50
Query on F50

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B],
S [auth E]
ETHANEPEROXOIC ACID
C2 H4 O3
KFSLWBXXFJQRDL-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
O [auth E],
T [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SME
Query on SME
D
L-PEPTIDE LINKINGC5 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 218.213α = 90
b = 218.213β = 90
c = 361.94γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1008736

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-02-28
    Changes: Database references
  • Version 1.2: 2018-03-07
    Changes: Database references
  • Version 1.3: 2019-10-23
    Changes: Data collection, Derived calculations
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence
  • Version 2.0: 2022-05-25
    Changes: Database references, Derived calculations, Non-polymer description
  • Version 2.1: 2023-10-04
    Changes: Data collection, Refinement description