4E9U

Crystal structure of dehydrosqualene synthase (Crtm) from S. aureus complexed with a thiocyanate inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4E9U/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-03-21 Released: 2012-04-25 
• Deposition Author(s): Lin, F.-Y., Axelson, J., Liu, Y.-L., Zhnag, Y., Oldfield, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.236 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

Head-to-Head Prenyl Tranferases: Anti-Infective Drug Targets.

Lin, F.Y., Liu, Y.L., Li, K., Cao, R., Zhu, W., Axelson, J., Pang, R., Oldfield, E.

(2012) J Med Chem 55: 4367-4372

• PubMed: 22486710 
• DOI: https://doi.org/10.1021/jm300208p
• Primary Citation of Related Structures:  
  4E9U, 4E9Z, 4EA0, 4EA1, 4EA2


• PubMed Abstract: 
  

  We report X-ray crystallographic structures of three inhibitors bound to dehydrosqualene synthase from Staphylococcus aureus: 1 (BPH-651), 2 (WC-9), and 3 (SQ-109). Compound 2 binds to the S2 site with its -SCN group surrounded by four hydrogen bond donors. With 1, we report two structures: in both, the quinuclidine headgroup binds in the allylic (S1) site with the side chain in S2, but in the presence of PPi and Mg(2+), the quinuclidine's cationic center interacts with PPi and three Mg(2+), mimicking a transition state involved in diphosphate ionization. With 3, there are again two structures. In one, the geranyl side chain binds to either S1 or S2 and the adamantane headgroup binds to S1. In the second, the side chain binds to S2 while the headgroup binds to S1. These results provide structural clues for the mechanism and inhibition of the head-to-head prenyl transferases and should aid future drug design.

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Organizational Affiliation: 

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

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: 34.66 kDa 
• Atom Count: 2,568 
• Modelled Residue Count: 284 
• Deposited Residue Count: 287 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehydrosqualene synthase	A	287	Staphylococcus aureus	Mutation(s): 0  Gene Names: crtM EC: 2.5.1.96
UniProt
Find proteins for A9JQL9 (Staphylococcus aureus) Explore A9JQL9  Go to UniProtKB:  A9JQL9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RWY	B [auth A]	2-(4-phenoxyphenoxy)ethyl thiocyanate C15 H13 N O2 S YQZHGQYIMXWEHI-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RWY	PDBBind:  4E9U	Ki: 1500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.236 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.44	α = 90
b = 80.44	β = 90
c = 90.793	γ = 120

Software Package:

Software Name	Purpose
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-25 
Deposition Author(s): Lin, F.-Y., Axelson, J., Liu, Y.-L., Zhnag, Y., Oldfield, E.

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2012-05-16
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations