1T9D

Crystal Structure Of Yeast Acetohydroxyacid Synthase In Complex With A Sulfonylurea Herbicide, Metsulfuron methyl


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    1T9A, 1T9B, 1T9C, 1T9D

  • 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acetolactate synthase, mitochondrialA, B, C, D677Saccharomyces cerevisiaeMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
AA [auth D],
H [auth A],
O [auth B],
T [auth C]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
1MM
Query on 1MM

Download Ideal Coordinates CCD File 
G [auth A],
N [auth B],
S [auth C],
V [auth C]
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
P25
Query on P25

Download Ideal Coordinates CCD File 
J [auth A],
M [auth B]
PENTYL TRIHYDROGEN DIPHOSPHATE
C5 H14 O7 P2
VFFCVKZHJFIUBM-UHFFFAOYSA-N
 Ligand Interaction
P22
Query on P22

Download Ideal Coordinates CCD File 
W [auth C],
Z [auth D]
ETHYL DIHYDROGEN DIPHOSPHATE
C2 H8 O7 P2
OJDJHGIXNZPZFD-UHFFFAOYSA-N
 Ligand Interaction
PYD
Query on PYD

Download Ideal Coordinates CCD File 
BA [auth D],
I [auth A],
P [auth B],
U [auth C]
2,5-DIMETHYL-PYRIMIDIN-4-YLAMINE
C6 H9 N3
UXKNAXNFIYFMIB-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
R [auth C],
Y [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1MM Binding MOAD:  1T9D Ki: 9.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 218.347α = 90
b = 218.347β = 90
c = 361.53γ = 90
Software Package:
Software NamePurpose
Adxvdata processing
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: Advisory, Refinement description