2GFX

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


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 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


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

  • 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 ...

    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. jun_wang2@merck.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-oxoacyl-[acyl-carrier-protein] synthase 2A427Escherichia coliMutation(s): 1 
Gene Names: fabFfabJ
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AAI5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PMN
Query on PMN

Download Ideal Coordinates CCD File 
B [auth A]PLATENSIMYCIN
C24 H27 N O7
CSOMAHTTWTVBFL-OFBLZTNGSA-N
 Ligand Interaction
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 = 75.727α = 90
b = 75.727β = 90
c = 147.304γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
MOLREPphasing
BUSTER-TNTrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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