1YI1

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

• PDB DOI:  https://doi.org/10.2210/pdb1YI1/pdb

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-01-10 Released: 2006-01-17 
• Deposition Author(s): McCourt, J.A., Pang, S.S., King-Scott, J., Guddat, L.W., Duggleby, R.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.187 
• R-Value Observed: 0.191 

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

• PubMed: 16407096 
• DOI: https://doi.org/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 2.2.1.6). 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.21 kDa 
• Atom Count: 4,727 
• Modelled Residue Count: 582 
• Deposited Residue Count: 590 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetolactate synthase	A	590	Arabidopsis thaliana	Mutation(s): 1  Gene Names: ILVB, ALS, AHAS, CSR1, TZP5, At3g48560, T8P19.70 EC: 2.2.1.6
UniProt
Find proteins for P17597 (Arabidopsis thaliana) Explore P17597  Go to UniProtKB:  P17597

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	F [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
1TB	C [auth A]	METHYL 2-[4-METHOXY-6-METHYL-1,3,5-TRAZIN-2-YL(METHYL)CARBAMOYLSULFAMOYL]BENZOATE C15 H17 N5 O6 S VLCQZHSMCYCDJL-UHFFFAOYSA-N
NHE	D [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
P22	E [auth A]	ETHYL DIHYDROGEN DIPHOSPHATE C2 H8 O7 P2 OJDJHGIXNZPZFD-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
1TB	BindingDB:  1YI1	Ki: 253 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.187 
• R-Value Observed: 0.191 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.06	α = 90
b = 179.06	β = 90
c = 186.145	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-17 
Deposition Author(s): McCourt, J.A., Pang, S.S., King-Scott, J., Guddat, L.W., Duggleby, R.G.

Revision History  

• 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