3JRX

Crystal structure of the BC domain of ACC2 in complex with soraphen A

• PDB DOI:  https://doi.org/10.2210/pdb3JRX/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-09-09 Released: 2010-01-12 
• Deposition Author(s): Cho, Y.S., Lee, J.I., Shin, D., Kim, H.T., Lee, T.G., Heo, Y.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.266 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 

Literature

Molecular mechanism for the regulation of human ACC2 through phosphorylation by AMPK.

Cho, Y.S., Lee, J.I., Shin, D., Kim, H.T., Jung, H.Y., Lee, T.G., Kang, L.W., Ahn, Y.J., Cho, H.S., Heo, Y.S.

(2010) Biochem Biophys Res Commun 391: 187-192

• PubMed: 19900410 
• DOI: https://doi.org/10.1016/j.bbrc.2009.11.029
• Primary Citation of Related Structures:  
  3JRW, 3JRX


• PubMed Abstract: 
  

  Acetyl-CoA carboxylases (ACCs) have been highlighted as therapeutic targets for obesity and diabetes, as they play crucial roles in fatty acid metabolism. ACC activity is regulated through the short-term mechanism of inactivation by reversible phosphorylation. Here, we report the crystal structures of the biotin carboxylase (BC) domain of human ACC2 phosphorylated by AMP-activated protein kinase (AMPK). The phosphorylated Ser222 binds to the putative dimer interface of BC, disrupting polymerization and providing the molecular mechanism of inactivation by AMPK. We also determined the structure of the human BC domain in complex with soraphen A, a macrocyclic polyketide natural product. This structure shows that the compound binds to the binding site of phosphorylated Ser222, implying that its inhibition mechanism is the same as that of phosphorylation by AMPK.

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Organizational Affiliation: 

R&D Center, CrystalGenomics, Inc., Seoul 138-739, Republic of Korea.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 65.94 kDa 
• Atom Count: 4,011 
• Modelled Residue Count: 496 
• Deposited Residue Count: 587 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA carboxylase 2	A	587	Homo sapiens	Mutation(s): 0  Gene Names: ACACB, ACC2, ACCB EC: 6.4.1.2 (PDB Primary Data), 6.3.4.14 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O00763 (Homo sapiens) Explore O00763  Go to UniProtKB:  O00763
PHAROS:  O00763

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S1A	B [auth A]	SORAPHEN A C29 H44 O8 WPMGNXPRKGXGBO-OFQQMTDKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
S1A	PDBBind:  3JRX	Kd: 1 (nM) from 1 assay(s)
	Binding MOAD:  3JRX	Kd: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.266 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.744	α = 90
b = 74.744	β = 90
c = 179.414	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-12 
Deposition Author(s): Cho, Y.S., Lee, J.I., Shin, D., Kim, H.T., Lee, T.G., Heo, Y.S.

Revision History  

• Version 1.0: 2010-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description