1OD2

Acetyl-CoA Carboxylase Carboxyltransferase Domain

• PDB DOI: https://doi.org/10.2210/pdb1OD2/pdb

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


• Deposited: 2003-02-12 Released: 2003-04-03 
• Deposition Author(s): Zhang, H., Yang, Z., Shen, Y., Tong, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.279 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Literature

Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase.

Zhang, H., Yang, Z., Shen, Y., Tong, L.

(2003) Science 299: 2064-2067

• PubMed: 12663926 
• DOI: https://doi.org/10.1126/science.1081366
• Primary Citation of Related Structures:  
  1OD2, 1OD4


• PubMed Abstract: 
  

  Acetyl-coenzyme A carboxylases (ACCs) are required for the biosynthesis and oxidation of long-chain fatty acids. They are targets for therapeutics against obesity and diabetes, and several herbicides function by inhibiting their carboxyltransferase (CT) domain. We determined the crystal structure of the free enzyme and the coenzyme A complex of yeast CT at 2.7 angstrom resolution and found that it comprises two domains, both belonging to the crotonase/ClpP superfamily. The active site is at the interface of a dimer. Mutagenesis and kinetic studies reveal the functional roles of conserved residues here. The herbicides target the active site of CT, providing a lead for inhibitor development against human ACCs.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 184.93 kDa 
• Atom Count: 11,433 
• Modelled Residue Count: 1,416 
• Deposited Residue Count: 1,610 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACETYL-COENZYME A CARBOXYLASE	A, B	805	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACO	C [auth A]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
ADE	D [auth B]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.279 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.87	α = 90
b = 138.13	β = 114.42
c = 101.4	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-03 
Deposition Author(s): Zhang, H., Yang, Z., Shen, Y., Tong, L.

Revision History  

• Version 1.0: 2003-04-03
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-05
  Changes: Refinement description
• Version 1.4: 2018-06-13
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary