3VJE

Crystal structure of the Y248A mutant of C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus in complex with zaragozic acid A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

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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:  
    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 ...

    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.


    Related Citations: 
    • A cholesterol biosynthesis inhibitor blocks Staphylococcus aureus virulence
      Liu, C.I., Liu, G.Y., Song, Y., Yin, F., Hensler, M.E., Jeng, W.Y., Nizet, V., Wang, A.H.J., Oldfield, E.
      (2008) Science 319: 1391
    • Inhibition of staphyloxanthin virulence factor biosynthesis in Staphylococcus aureus: in vitro, in vivo, and crystallographic results
      Song, Y., Liu, C.I., Lin, F.Y., No, J.H., Hensler, M., Liu, Y.L., Jeng, W.Y., Low, J., Liu, G.Y., Nizet, V., Wang, A.H.J., Oldfield, E.
      (2009) J Med Chem 52: 3869
    • Mechanism of action and inhibition of dehydrosqualene synthase
      Lin, F.Y., Liu, C.I., Liu, Y.L., Zhang, Y., Wang, K., Jeng, W.Y., Ko, T.P., Cao, R., Wang, A.H.J., Oldfield, E.
      (2010) Proc Natl Acad Sci U S A 107: 21337

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dehydrosqualene synthaseA, B293Staphylococcus aureusMutation(s): 1 
Gene Names: crtM
EC: 2.5.1 (PDB Primary Data), 2.5.1.96 (UniProt)
UniProt
Find proteins for A9JQL9 (Staphylococcus aureus)
Explore A9JQL9 
Go to UniProtKB:  A9JQL9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZGA (Subject of Investigation/LOI)
Query on ZGA

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]Zaragozic acid A
C35 H46 O14
DFKDOZMCHOGOBR-NCSQYGPNSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ZGA PDBBind:  3VJE Kd: 9.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.177α = 90
b = 80.177β = 90
c = 185.414γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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