1T9B

Crystal structure of yeast acetohydroxyacid synthase in complex with a sulfonylurea herbicide, chlorsulfuron


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Elucidating the specificity of binding of sulfonylurea herbicides to acetohydroxyacid synthase.

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

(2005) Biochemistry 44: 2330-2338

  • DOI: 10.1021/bi047980a
  • Primary Citation of Related Structures:  
    1T9D, 1T9C, 1T9B, 1T9A

  • PubMed Abstract: 
  • Acetohydroxyacid synthase (AHAS, EC 2.2.1.6) is the target for the sulfonylurea herbicides, which act as potent inhibitors of the enzyme. Chlorsulfuron (marketed as Glean) and sulfometuron methyl (marketed as Oust) are two commercially important members of this family of herbicides ...

    Acetohydroxyacid synthase (AHAS, EC 2.2.1.6) is the target for the sulfonylurea herbicides, which act as potent inhibitors of the enzyme. Chlorsulfuron (marketed as Glean) and sulfometuron methyl (marketed as Oust) are two commercially important members of this family of herbicides. Here we report crystal structures of yeast AHAS in complex with chlorsulfuron (at a resolution of 2.19 A), sulfometuron methyl (2.34 A), and two other sulfonylureas, metsulfuron methyl (2.29 A) and tribenuron methyl (2.58 A). The structures observed suggest why these inhibitors have different potencies and provide clues about the differential effects of mutations in the active site tunnel on various inhibitors. In all of the structures, the thiamin diphosphate cofactor is fragmented, possibly as the result of inhibitor binding. In addition to thiamin diphosphate, AHAS requires FAD for activity. Recently, it has been reported that reduction of FAD can occur as a minor side reaction due to reaction with the carbanion/enamine of the hydroxyethyl-ThDP intermediate that is formed midway through the catalytic cycle. Here we report that the isoalloxazine ring has a bent conformation that would account for its ability to accept electrons from the hydroxyethyl intermediate. Most sequence and mutation data suggest that yeast AHAS is a high-quality model for the plant enzyme.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Queensland, Brisbane, Queensland 4072, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acetolactate synthase, mitochondrialA, B677Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ILV2SMR1YMR108WYM9718.07
EC: 2.2.1.6
Find proteins for P07342 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07342 
Go to UniProtKB:  P07342
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
F [auth A], N [auth B]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
1CS
Query on 1CS

Download Ideal Coordinates CCD File 
E [auth A], M [auth B]1-(2-CHLOROPHENYLSULFONYL)-3-(4-METHOXY-6-METHYL-L,3,5-TRIAZIN-2-YL)UREA
C12 H12 Cl N5 O4 S
VJYIFXVZLXQVHO-UHFFFAOYSA-N
 Ligand Interaction
P25
Query on P25

Download Ideal Coordinates CCD File 
L [auth B]PENTYL TRIHYDROGEN DIPHOSPHATE
C5 H14 O7 P2
VFFCVKZHJFIUBM-UHFFFAOYSA-N
 Ligand Interaction
YF3
Query on YF3

Download Ideal Coordinates CCD File 
I [auth A]2-{[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]AMINO}PROPANE-1-THIOL
C9 H16 N4 S
BGGAKPFEDJLRDQ-UHFFFAOYSA-N
 Ligand Interaction
P22
Query on P22

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

Download Ideal Coordinates CCD File 
G [auth A]5-(AMINOMETHYL)-2-METHYLPYRIMIDIN-4-AMINE
C6 H10 N4
OZOHTVFCSKFMLL-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A], J [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A], K [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1CSKi:  127   nM  Binding MOAD
1CSKi:  127   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 
  • Space Group: P 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.579α = 90
b = 154.579β = 90
c = 178.759γ = 90
Software Package:
Software NamePurpose
Adxvdata processing
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description