Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 45.10 kDa 
• Atom Count: 3150 
• Modelled Residue Count: 411 
• Deposited Residue Count: 427 
• Unique protein chains: 1

2GFX

Structure of E. coli FabF(C163Q) in complex with Platensimycin

• PDB DOI: 10.2210/pdb2GFX/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-03-23 Released: 2006-05-23 
• Deposition Author(s): Soisson, S.M., Parthasarathy, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.255 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

Literature

Platensimycin is a selective FabF inhibitor with potent antibiotic properties.

Wang, J., Soisson, S.M., Young, K., Shoop, W., Kodali, S., Galgoci, A., Painter, R., Parthasarathy, G., Tang, Y.S., Cummings, R., Ha, S., Dorso, K., Motyl, M., Jayasuriya, H., Ondeyka, J., Herath, K., Zhang, C., Hernandez, L., Allocco, J., Basilio, A., Tormo, J.R., Genilloud, O., Vicente, F., Pelaez, F., Colwell, L., Lee, S.H., Michael, B., Felcetto, T., Gill, C., Silver, L.L., Hermes, J.D., Bartizal, K., Barrett, J., Schmatz, D., Becker, J.W., Cully, D., Singh, S.B.

(2006) Nature 441: 358-361

• PubMed: 16710421 
• DOI: 10.1038/nature04784
• Primary Citation of Related Structures:  
  2GFV, 2GFW, 2GFX, 2GFY


• PubMed Abstract: 
  

Bacterial infection remains a serious threat to human lives because of emerging resistance to existing antibiotics. Although the scientific community has avidly pursued the discovery of new antibiotics that interact with new targets, these efforts have met with limited success since the early 1960s. Here we report the discovery of platensimycin, a previously unknown class of antibiotics produced by Streptomyces platensis. Platensimycin demonstrates strong, broad-spectrum Gram-positive antibacterial activity by selectively inhibiting cellular lipid biosynthesis. We show that this anti-bacterial effect is exerted through the selective targeting of beta-ketoacyl-(acyl-carrier-protein (ACP)) synthase I/II (FabF/B) in the synthetic pathway of fatty acids. Direct binding assays show that platensimycin interacts specifically with the acyl-enzyme intermediate of the target protein, and X-ray crystallographic studies reveal that a specific conformational change that occurs on acylation must take place before the inhibitor can bind. Treatment with platensimycin eradicates Staphylococcus aureus infection in mice. Because of its unique mode of action, platensimycin shows no cross-resistance to other key antibiotic-resistant strains tested, including methicillin-resistant S. aureus, vancomycin-intermediate S. aureus and vancomycin-resistant enterococci. Platensimycin is the most potent inhibitor reported for the FabF/B condensing enzymes, and is the only inhibitor of these targets that shows broad-spectrum activity, in vivo efficacy and no observed toxicity.

---

Organizational Affiliation: 

Merck Research Laboratories, Rahway, New Jersey 07065, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 2	A	427	Escherichia coli	Mutation(s): 1  Gene Names: fabF, fabJ EC: 2.3.1.41 (PDB Primary Data), 2.3.1.179 (UniProt)
UniProt
Find proteins for P0AAI5 (Escherichia coli (strain K12)) Explore P0AAI5  Go to UniProtKB:  P0AAI5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PMN	B [auth A]	PLATENSIMYCIN C24 H27 N O7 CSOMAHTTWTVBFL-OFBLZTNGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.255 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.727	α = 90
b = 75.727	β = 90
c = 147.304	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
HKL-2000	data reduction
MOLREP	phasing
BUSTER-TNT	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-03-23 
• Released Date: 2006-05-23 
Deposition Author(s): Soisson, S.M., Parthasarathy, G.

Revision History  

• Version 1.0: 2006-05-23
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 2.0: 2021-10-20
  Changes: Atomic model, Database references, Derived calculations