Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Helical - H  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 258.66 kDa 
• Atom Count: 17693 
• Modelled Residue Count: 2045 
• Deposited Residue Count: 2274 
• Unique protein chains: 1

3K8X

Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in complex with tepraloxydim

• PDB DOI: 10.2210/pdb3K8X/pdb

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


• Deposited: 2009-10-15 Released: 2009-12-01 
• Deposition Author(s): Xiang, S., Callaghan, M.M., Watson, K.G., Tong, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.221 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

A different mechanism for the inhibition of the carboxyltransferase domain of acetyl-coenzyme A carboxylase by tepraloxydim.

Xiang, S., Callaghan, M.M., Watson, K.G., Tong, L.

(2009) Proc Natl Acad Sci U S A 106: 20723-20727

• PubMed: 19926852 
• DOI: 10.1073/pnas.0908431106
• Primary Citation of Related Structures:  
  3K8X


• PubMed Abstract: 
  

Acetyl-CoA carboxylases (ACCs) are crucial metabolic enzymes and are attractive targets for drug discovery. Haloxyfop and tepraloxydim belong to two distinct classes of commercial herbicides and kill sensitive plants by inhibiting the carboxyltransferase (CT) activity of ACC. Our earlier structural studies showed that haloxyfop is bound near the active site of the CT domain, at the interface of its dimer, and a large conformational change in the dimer interface is required for haloxyfop binding. We report here the crystal structure at 2.3 A resolution of the CT domain of yeast ACC in complex with tepraloxydim. The compound has a different mechanism of inhibiting the CT activity compared to haloxyfop, as well as the mammalian ACC inhibitor CP-640186. Tepraloxydim probes a different region of the dimer interface and requires only small but important conformational changes in the enzyme, in contrast to haloxyfop. The binding mode of tepraloxydim explains the structure-activity relationship of these inhibitors, and provides a molecular basis for their distinct sensitivity to some of the resistance mutations, as compared to haloxyfop. Despite the chemical diversity between haloxyfop and tepraloxydim, the compounds do share two binding interactions to the enzyme, which may be important anchoring points for the development of ACC inhibitors.

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Organizational Affiliation: 

Department of Biological Sciences, Columbia University, New York, NY 10027, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA carboxylase	A, B, C	758	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: ACC1, ACETYL-COA CARBOXYLASE, FAS3, N3175, YNR016C EC: 6.4.1.2 (PDB Primary Data), 6.3.4.14 (PDB Primary Data)
UniProt
Find proteins for Q00955 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q00955  Go to UniProtKB:  Q00955

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B89	D [auth A], E [auth B], F [auth C]	(5S)-2-[(1E)-N-{[(2E)-3-chloroprop-2-en-1-yl]oxy}propanimidoyl]-3-hydroxy-5-(tetrahydro-2H-pyran-4-yl)cyclohex-2-en-1-one C17 H24 Cl N O4 IOYNQIMAUDJVEI-FGWLPLFYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.221 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 247.303	α = 90
b = 124.797	β = 94.32
c = 145.369	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-15 
• Released Date: 2009-12-01 
Deposition Author(s): Xiang, S., Callaghan, M.M., Watson, K.G., Tong, L.

Revision History  

• Version 1.0: 2009-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance