3VJ9

Crystal structure of the human squalene synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1074/jbc.M112.351254
  • Primary Citation of Related Structures:  

  • 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 antili ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Squalene synthase
A
343Homo sapiensMutation(s): 0 
Gene Names: FDFT1
EC: 2.5.1.21
Find proteins for P37268 (Homo sapiens)
Go to Gene View: FDFT1
Go to UniProtKB:  P37268
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.776α = 90.00
b = 76.657β = 90.00
c = 82.501γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
MOLREPphasing
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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