1W96

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

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 

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This is version 1.2 of the entry. See complete history. 


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

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

  • 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 ...

    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.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ACETYL-COENZYME A CARBOXYLASEA, B, C554Saccharomyces cerevisiaeMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S1A (Subject of Investigation/LOI)
Query on S1A
Download Ideal Coordinates CCD File 
 D [auth A], E [auth B], F [auth C]SORAPHEN A
C29 H44 O8
WPMGNXPRKGXGBO-OFQQMTDKSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
S1AKd:  3.9000000953674316   nM  Binding MOAD
S1AKd :  3.9000000953674316   nM  PDBBind
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 = 63.83α = 90
b = 96.52β = 96.82
c = 139.95γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKLdata reduction
HKLdata scaling
SOLVE/RESOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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