5FEM | pdb_00005fem

Saccharomyces cerevisiae Acetohydroxyacid Synthase in complex with bensulfuron methyl

PDB DOI: https://doi.org/10.2210/pdb5FEM/pdb

Classification: TRANSFERASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-12-17 Released: 2016-03-16
Deposition Author(s): Guddat, L.W., Lonhienne, T.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.173 (Depositor), 0.176 (DCC)
R-Value Work:
0.150 (Depositor), 0.154 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Commercial Herbicides Can Trigger the Oxidative Inactivation of Acetohydroxyacid Synthase.

Lonhienne, T., Nouwens, A., Williams, C.M., Fraser, J.A., Lee, Y.T., West, N.P., Guddat, L.W.

(2016) Angew Chem Int Ed Engl 55: 4247-4251

PubMed: 26924714 Search on PubMed
DOI: https://doi.org/10.1002/anie.201511985
Primary Citation Related Structures:
5FEM

PubMed Abstract:
Acetohydroxyacid synthase (AHAS) inhibitors are highly successful commercial herbicides. New kinetic data show that the binding of these compounds leads to reversible accumulative inhibition of AHAS. Crystallographic data (to a resolution of 2.17 Å) for an AHAS-herbicide complex shows that closure of the active site occurs when the herbicidal inhibitor binds, thus preventing exchange with solvent. This feature combined with new kinetic data shows that molecular oxygen promotes an accumulative inhibition leading to the conclusion that the exceptional potency of these herbicides is augmented by subversion of an inherent oxygenase side reaction. The reactive oxygen species produced by this reaction are trapped in the active site, triggering oxidation reactions that ultimately lead to the alteration of the redox state of the cofactor flavin adenine dinucleotide (FAD), a feature that accounts for the observed reversible accumulative inhibition.

Organizational Affiliation

School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072 QLD, Australia. t.lonhienne@uq.edu.au.

Macromolecule Content

Total Structure Weight: 150.54 kDa
Atom Count: 9,937
Modeled Residue Count: 1,198
Deposited Residue Count: 1,354
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetolactate synthase catalytic subunit, mitochondrial	A, B	677	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: ILV2, SMR1, YMR108W, YM9718.07 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07342
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
TPP Query on TPP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
60G Query on 60G Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B]	methyl 2-[(4,6-dimethoxypyrimidin-2-yl)carbamoylsulfamoylmethyl]benzoate C₁₆ H₁₈ N₄ O₇ S XMQFTWRPUQYINF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain F [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain C [auth A]	C [auth A], F [auth A], I [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
60G	BindingDB: 5FEM	Ki: 4.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free: 0.173 (Depositor), 0.176 (DCC)
R-Value Work: 0.150 (Depositor), 0.154 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.673	α = 90
b = 154.673	β = 90
c = 178.385	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-03-16

Deposition Author(s):

Guddat, L.W.

Lonhienne, T.

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1087713

Revision History (Full details and data files)

Version 1.0: 2016-03-16
Type: Initial release
Version 1.1: 2016-04-06
Changes: Database references
Version 1.2: 2017-09-27
Changes: Author supporting evidence, Data collection, Database references, Derived calculations
Version 1.3: 2018-05-23
Changes: Data collection, Structure summary
Version 1.4: 2020-01-08
Changes: Author supporting evidence
Version 1.5: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description