2ZCS

Crystal structure of the C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus complexed with bisphosphonate BPH-700

• PDB DOI: https://doi.org/10.2210/pdb2ZCS/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-11-11 Released: 2008-03-11 
• Deposition Author(s): Liu, C.I., Jeng, W.Y., Wang, A.H., Oldfield, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.246 
• R-Value Work: 0.198 

Starting Model: experimental

Literature

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: 1391-1394

• PubMed: 18276850 
• DOI: https://doi.org/10.1126/science.1153018
• Primary Citation of Related Structures:  
  2ZCO, 2ZCQ, 2ZCR, 2ZCS, 3W7F


• PubMed Abstract: 
  

  Staphylococcus aureus produces hospital- and community-acquired infections, with methicillin-resistant S. aureus posing a serious public health threat. The golden carotenoid pigment of S. aureus, staphyloxanthin, promotes resistance to reactive oxygen species and host neutrophil-based killing, and early enzymatic steps in staphyloxanthin production resemble those for cholesterol biosynthesis. We determined the crystal structures of S. aureus dehydrosqualene synthase (CrtM) at 1.58 angstrom resolution, finding structural similarity to human squalene synthase (SQS). We screened nine SQS inhibitors and determined the structures of three, bound to CrtM. One, previously tested for cholesterol-lowering activity in humans, blocked staphyloxanthin biosynthesis in vitro (median inhibitory concentration approximately 100 nM), resulting in colorless bacteria with increased susceptibility to killing by human blood and to innate immune clearance in a mouse infection model. This finding represents proof of principle for a virulence factor-based therapy against S. aureus.

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Organizational Affiliation: 

Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 11529, Taiwan.

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: 35.27 kDa 
• Atom Count: 2,755 
• Modelled Residue Count: 284 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehydrosqualene synthase	A	293	Staphylococcus aureus	Mutation(s): 0  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B70	B [auth A]	tripotassium (1R)-4-biphenyl-4-yl-1-phosphonatobutane-1-sulfonate C16 H16 K3 O6 P S LBNUOQAEVSXSSE-UFRNLTNDSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
B70	PDBBind:  2ZCS	Ki: 6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.246 
• R-Value Work: 0.198 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.57	α = 90
b = 80.57	β = 90
c = 90.74	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: 2008-03-11 
Deposition Author(s): Liu, C.I., Jeng, W.Y., Wang, A.H., Oldfield, E.

Revision History  

• Version 1.0: 2008-03-11
  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