3ACX

Crystal structure of the C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus complexed with BPH-673


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 21337-21342

  • DOI: 10.1073/pnas.1010907107
  • Primary Citation of Related Structures:  
    3LGZ, 3NPR, 3NRI, 3AE0, 3ACW, 3ACX, 3ACY, 3ADZ

  • PubMed Abstract: 
  • "Head-to-head" terpene synthases catalyze the first committed steps in sterol and carotenoid biosynthesis: the condensation of two isoprenoid diphosphates to form cyclopropylcarbinyl diphosphates, followed by ring opening. Here, we report the structures of Staphylococcus aureus dehydrosqualene synthase (CrtM) complexed with its reaction intermediate, presqualene diphosphate (PSPP), the dehydrosqualene (DHS) product, as well as a series of inhibitors ...

    "Head-to-head" terpene synthases catalyze the first committed steps in sterol and carotenoid biosynthesis: the condensation of two isoprenoid diphosphates to form cyclopropylcarbinyl diphosphates, followed by ring opening. Here, we report the structures of Staphylococcus aureus dehydrosqualene synthase (CrtM) complexed with its reaction intermediate, presqualene diphosphate (PSPP), the dehydrosqualene (DHS) product, as well as a series of inhibitors. The results indicate that, on initial diphosphate loss, the primary carbocation so formed bends down into the interior of the protein to react with C2,3 double bond in the prenyl acceptor to form PSPP, with the lower two-thirds of both PSPP chains occupying essentially the same positions as found in the two farnesyl chains in the substrates. The second-half reaction is then initiated by the PSPP diphosphate returning back to the Mg(2+) cluster for ionization, with the resultant DHS so formed being trapped in a surface pocket. This mechanism is supported by the observation that cationic inhibitors (of interest as antiinfectives) bind with their positive charge located in the same region as the cyclopropyl carbinyl group; that S-thiolo-diphosphates only inhibit when in the allylic site; activity results on 11 mutants show that both DXXXD conserved domains are essential for PSPP ionization; and the observation that head-to-tail isoprenoid synthases as well as terpene cyclases have ionization and alkene-donor sites which spatially overlap those found in CrtM.


    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., 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., Oldfield, E.
      (2009) J Med Chem 52: 3869

    Organizational Affiliation

    Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dehydrosqualene synthaseA293Staphylococcus aureusMutation(s): 0 
Gene Names: crtM
EC: 2.5.1 (PDB Primary Data), 2.5.1.96 (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
673
Query on 673

Download Ideal Coordinates CCD File 
B [auth A]N-(1-methylethyl)-3-[(3-prop-2-en-1-ylbiphenyl-4-yl)oxy]propan-1-amine
C21 H27 N O
CKIDETHAWPUGOQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
673Ki :  2000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.628α = 90
b = 80.628β = 90
c = 90.453γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-10-30
    Changes: Database references