1YHY

Crystal structure of Arabidopsis thaliana Acetohydroxyacid synthase In Complex With A Sulfonylurea Herbicide, Metsulfuron methyl


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Herbicide-binding sites revealed in the structure of plant acetohydroxyacid synthase

McCourt, J.A.Pang, S.S.King-Scott, J.Guddat, L.W.Duggleby, R.G.

(2006) Proc Natl Acad Sci U S A 103: 569-573

  • DOI: 10.1073/pnas.0508701103
  • Primary Citation of Related Structures:  
    1YBH, 1YHY, 1YHZ, 1YI0, 1YI1, 1Z8N

  • PubMed Abstract: 
  • The sulfonylureas and imidazolinones are potent commercial herbicide families. They are among the most popular choices for farmers worldwide, because they are nontoxic to animals and highly selective. These herbicides inhibit branched-chain amino acid biosynthesis in plants by targeting acetohydroxyacid synthase (AHAS, EC 2 ...

    The sulfonylureas and imidazolinones are potent commercial herbicide families. They are among the most popular choices for farmers worldwide, because they are nontoxic to animals and highly selective. These herbicides inhibit branched-chain amino acid biosynthesis in plants by targeting acetohydroxyacid synthase (AHAS, EC 2.2.1.6). This report describes the 3D structure of Arabidopsis thaliana AHAS in complex with five sulfonylureas (to 2.5 A resolution) and with the imidazolinone, imazaquin (IQ; 2.8 A). Neither class of molecule has a structure that mimics the substrates for the enzyme, but both inhibit by blocking a channel through which access to the active site is gained. The sulfonylureas approach within 5 A of the catalytic center, which is the C2 atom of the cofactor thiamin diphosphate, whereas IQ is at least 7 A from this atom. Ten of the amino acid residues that bind the sulfonylureas also bind IQ. Six additional residues interact only with the sulfonylureas, whereas there are two residues that bind IQ but not the sulfonylureas. Thus, the two classes of inhibitor occupy partially overlapping sites but adopt different modes of binding. The increasing emergence of resistant weeds due to the appearance of mutations that interfere with the inhibition of AHAS is now a worldwide problem. The structures described here provide a rational molecular basis for understanding these mutations, thus allowing more sophisticated AHAS inhibitors to be developed. There is no previously described structure for any plant protein in complex with a commercial herbicide.


    Organizational Affiliation

    School of Molecular and Microbial Sciences, University of Queensland, Brisbane QLD 4072, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acetolactate synthaseA590Arabidopsis thalianaMutation(s): 1 
Gene Names: ILVBALSAHASCSR1TZP5At3g48560T8P19.70
EC: 2.2.1.6
UniProt
Find proteins for P17597 (Arabidopsis thaliana)
Explore P17597 
Go to UniProtKB:  P17597
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
E [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
1MM (Subject of Investigation/LOI)
Query on 1MM

Download Ideal Coordinates CCD File 
C [auth A]METHYL 2-[({[(4-METHOXY-6-METHYL-1,3,5-TRIAZIN-2-YL)AMINO]CARBONYL}AMINO)SULFONYL]BENZOATE
C14 H15 N5 O6 S
RSMUVYRMZCOLBH-UHFFFAOYSA-N
 Ligand Interaction
NHE
Query on NHE

Download Ideal Coordinates CCD File 
D [auth A]2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
 Ligand Interaction
P22 (Subject of Investigation/LOI)
Query on P22

Download Ideal Coordinates CCD File 
F [auth A]ETHYL DIHYDROGEN DIPHOSPHATE
C2 H8 O7 P2
OJDJHGIXNZPZFD-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
AL-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.226α = 90
b = 178.226β = 90
c = 185.248γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance