1N0H

Crystal Structure of Yeast Acetohydroxyacid Synthase in Complex with a Sulfonylurea Herbicide, Chlorimuron Ethyl


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular basis of sulfonylurea herbicide inhibition of acetohydroxyacid synthase

Pang, S.S.Guddat, L.W.Duggleby, R.G.

(2003) J Biol Chem 278: 7639-7644

  • DOI: 10.1074/jbc.M304038200
  • Primary Citation of Related Structures:  
    1N0H, 1OZH, 1OZG, 1OZF

  • PubMed Abstract: 
  • Acetohydroxyacid synthase (AHAS) and acetolactate synthase (ALS) are thiamine diphosphate (ThDP)-dependent enzymes that catalyze the decarboxylation of pyruvate to give a cofactor-bound hydroxyethyl group, which is transferred to a second molecule of pyruvate to give 2-acetolactate ...

    Acetohydroxyacid synthase (AHAS) and acetolactate synthase (ALS) are thiamine diphosphate (ThDP)-dependent enzymes that catalyze the decarboxylation of pyruvate to give a cofactor-bound hydroxyethyl group, which is transferred to a second molecule of pyruvate to give 2-acetolactate. AHAS is found in plants, fungi, and bacteria, is involved in the biosynthesis of the branched-chain amino acids, and contains non-catalytic FAD. ALS is found only in some bacteria, is a catabolic enzyme required for the butanediol fermentation, and does not contain FAD. Here we report the 2.3-A crystal structure of Klebsiella pneumoniae ALS. The overall structure is similar to AHAS except for a groove that accommodates FAD in AHAS, which is filled with amino acid side chains in ALS. The ThDP cofactor has an unusual conformation that is unprecedented among the 26 known three-dimensional structures of nine ThDP-dependent enzymes, including AHAS. This conformation suggests a novel mechanism for ALS. A second structure, at 2.0 A, is described in which the enzyme is trapped halfway through the catalytic cycle so that it contains the hydroxyethyl intermediate bound to ThDP. The cofactor has a tricyclic structure that has not been observed previously in any ThDP-dependent enzyme, although similar structures are well known for free thiamine. This structure is consistent with our proposed mechanism and probably results from an intramolecular proton transfer within a tricyclic carbanion that is the true reaction intermediate. Modeling of the second molecule of pyruvate into the active site of the enzyme with the bound intermediate is consistent with the stereochemistry and specificity of ALS.


    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 synthaseA, B677Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ILV2
EC: 4.1.3.18 (PDB Primary Data), 2.2.1.6 (UniProt)
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 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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

Download Ideal Coordinates CCD File 
M [auth B]THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
CIE
Query on CIE

Download Ideal Coordinates CCD File 
E [auth A], K [auth B]2-[[[[(4-CHLORO-6-METHOXY-2-PYRIMIDINYL)AMINO]CARBONYL]AMINO]SULFONYL]BENZOIC ACID ETHYL ESTER
C15 H15 Cl N4 O6 S
NSWAMPCUPHPTTC-UHFFFAOYSA-N
 Ligand Interaction
AYD
Query on AYD

Download Ideal Coordinates CCD File 
G [auth A]4-{[(4'-AMINO-2'-METHYLPYRIMIDIN-5'-YL)METHYL]AMINO}PENT-3-ENYL DIPHOSPHATE
C11 H20 N4 O7 P2
DPGNBHAKLFOOJK-XBXARRHUSA-N
 Ligand Interaction
DTT
Query on DTT

Download Ideal Coordinates CCD File 
F [auth A], L [auth B]2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
K
Query on K

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

Download Ideal Coordinates CCD File 
D [auth A], J [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CIEKi:  3.299999952316284   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.168 
  • Space Group: P 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.976α = 90
b = 153.976β = 90
c = 178.298γ = 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: 2003-01-07
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description