Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 3  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 186.52 kDa 
• Atom Count: 14282 
• Modelled Residue Count: 1628 
• Deposited Residue Count: 1662 
• Unique protein chains: 1

1W96

Crystal Structure of Biotin Carboxylase Domain of Acetyl-coenzyme A Carboxylase from Saccharomyces cerevisiae in Complex with Soraphen A

• PDB DOI: 10.2210/pdb1W96/pdb

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


• Deposited: 2004-10-06 Released: 2005-01-04 
• Deposition Author(s): Shen, Y., Volrath, S.L., Weatherly, S.C., Elich, T.D., Tong, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.230 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 

Literature

A Mechanism for the Potent Inhibition of Eukaryotic Acetyl-Coenzyme a Carboxylase by Soraphen A, a Macrocyclic Polyketide Natural Product

Shen, Y., Volrath, S.L., Weatherly, S.C., Elich, T.D., Tong, L.

(2004) Mol Cell 16: 881

• PubMed: 15610732 
• DOI: 10.1016/j.molcel.2004.11.034
• Primary Citation of Related Structures:  
  1W93, 1W96


• PubMed Abstract: 
  

Acetyl-coenzyme A carboxylases (ACCs) have crucial roles in fatty acid metabolism. Soraphen A, a macrocyclic polyketide natural product, is a nanomolar inhibitor against the biotin carboxylase (BC) domain of human, yeast, and other eukaryotic ACCs. Here we report the crystal structures of the yeast BC domain, alone and in complex with soraphen A. Soraphen has extensive interactions with an allosteric site, about 25 A from the active site. The specificity of soraphen is explained by large structural differences between the eukaryotic and prokaryotic BC in its binding site, confirmed by our studies on the effects of single-site mutations in this binding site. Unexpectedly, our structures suggest that soraphen may bind in the BC dimer interface and inhibit the BC activity by disrupting the oligomerization of this domain. Observations from native gel electrophoresis confirm this structural insight. The structural information provides a foundation for structure-based design of new inhibitors against these enzymes.

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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-COENZYME A CARBOXYLASE	A, B, C	554	Saccharomyces cerevisiae	Mutation(s): 0  EC: 6.4.1.2 (PDB Primary Data), 6.3.4.14 (UniProt)
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
S1A	D [auth A], E [auth B], F [auth C]	SORAPHEN A C29 H44 O8 WPMGNXPRKGXGBO-OFQQMTDKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
S1A	PDBBind:  1W96	Kd: 3.9 (nM) from 1 assay(s)
	Binding MOAD:  1W96	Kd: 3.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.230 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.83	α = 90
b = 96.52	β = 96.82
c = 139.95	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL	data reduction
HKL	data scaling
SOLVE/RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-10-06 
• Released Date: 2005-01-04 
Deposition Author(s): Shen, Y., Volrath, S.L., Weatherly, S.C., Elich, T.D., Tong, L.

Revision History  

• Version 1.0: 2005-01-04
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance