Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 79.02 kDa 
• Atom Count: 5974 
• Residue Count: 669 
• Unique protein chains: 1

3VJA

Crystal structure of the human squalene synthase

• DOI: 10.2210/pdb3VJA/pdb

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


• Deposited: 2011-10-14 Released: 2012-04-11 
• Deposition Author(s): Liu, C.I., Jeng, W.Y., Chang, W.J., Wang, A.H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.233 
• R-Value Work: 0.165 
• R-Value Observed: 0.168 

Literature

Binding modes of zaragozic acid A to human squalene synthase and staphylococcal dehydrosqualene synthase

Liu, C.I., Jeng, W.Y., Chang, W.J., Ko, T.P., Wang, A.H.J.

(2012) J Biol Chem 287: 18750-18757

• PubMed: 22474324 
• DOI: 10.1074/jbc.M112.351254
• Primary Citation of Related Structures:  
  3VJA, 3VJB, 3VJC, 3VJD, 3VJE, 3VJ8, 3VJ9


• PubMed Abstract: 
  

Zaragozic acids (ZAs) belong to a family of fungal metabolites with nanomolar inhibitory activity toward squalene synthase (SQS). The enzyme catalyzes the committed step of sterol synthesis and has attracted attention as a potential target for antilipogenic and antiinfective therapies. Here, we have determined the structure of ZA-A complexed with human SQS. ZA-A binding induces a local conformational change in the substrate binding site, and its C-6 acyl group also extends over to the cofactor binding cavity. In addition, ZA-A effectively inhibits a homologous bacterial enzyme, dehydrosqualene synthase (CrtM), which synthesizes the precursor of staphyloxanthin in Staphylococcus aureus to cope with oxidative stress. Size reduction at Tyr(248) in CrtM further increases the ZA-A binding affinity, and it reveals a similar overall inhibitor binding mode to that of human SQS/ZA-A except for the C-6 acyl group. These structures pave the way for further improving selectivity and development of a new generation of anticholesterolemic and antimicrobial inhibitors.

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Organizational Affiliation: 

Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Squalene synthase	A, B	343	Homo sapiens	Mutation(s): 0  Gene Names: FDFT1 EC: 2.5.1.21
Find proteins for P37268 (Homo sapiens) Explore P37268  Go to UniProtKB:  P37268
NIH Common Fund Data Resources
PHAROS:  P37268 GTEx:  ENSG00000079459

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	A, B	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.233 
• R-Value Work: 0.165 
• R-Value Observed: 0.168 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.008	α = 90
b = 82.341	β = 91.57
c = 77.175	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-10-14 
• Released Date: 2012-04-11 
Deposition Author(s): Liu, C.I., Jeng, W.Y., Chang, W.J., Wang, A.H.J.

Revision History 

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2013-07-24
  Changes: Database references