6B89

E. coli LptB in complex with ADP and novobiocin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Antibiotic Novobiocin Binds and Activates the ATPase That Powers Lipopolysaccharide Transport.

May, J.M.Owens, T.W.Mandler, M.D.Simpson, B.W.Lazarus, M.B.Sherman, D.J.Davis, R.M.Okuda, S.Massefski, W.Ruiz, N.Kahne, D.

(2017) J. Am. Chem. Soc. 139: 17221-17224

  • DOI: 10.1021/jacs.7b07736
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Novobiocin is an orally active antibiotic that inhibits DNA gyrase by binding the ATP-binding site in the ATPase subunit. Although effective against Gram-positive pathogens, novobiocin has limited activity against Gram-negative organisms due to the p ...

    Novobiocin is an orally active antibiotic that inhibits DNA gyrase by binding the ATP-binding site in the ATPase subunit. Although effective against Gram-positive pathogens, novobiocin has limited activity against Gram-negative organisms due to the presence of the lipopolysaccharide-containing outer membrane, which acts as a permeability barrier. Using a novobiocin-sensitive Escherichia coli strain with a leaky outer membrane, we identified a mutant with increased resistance to novobiocin. Unexpectedly, the mutation that increases novobiocin resistance was not found to alter gyrase, but the ATPase that powers lipopolysaccharide (LPS) transport. Co-crystal structures, biochemical, and genetic evidence show novobiocin directly binds this ATPase. Novobiocin does not bind the ATP binding site but rather the interface between the ATPase subunits and the transmembrane subunits of the LPS transporter. This interaction increases the activity of the LPS transporter, which in turn alters the permeability of the outer membrane. We propose that novobiocin will be a useful tool for understanding how ATP hydrolysis is coupled to LPS transport.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipopolysaccharide export system ATP-binding protein LptB
A, B
249Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: lptB (yhbG)
EC: 3.6.3.-
Find proteins for P0A9V1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A9V1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NOV
Query on NOV

Download SDF File 
Download CCD File 
A, B
NOVOBIOCIN
4-Hydroxy-3-[4-hydroxy-3-(3-methylbut-2-enyl)benzamido]-8-methylcoumarin-7-yl 3-O-carbamoyl-5,5-di-C-methyl-alpha-l-lyxofuranoside
C31 H36 N2 O11
YJQPYGGHQPGBLI-KGSXXDOSSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 190.319α = 90.00
b = 35.100β = 91.52
c = 63.050γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata reduction
PHENIXrefinement
Aimlessdata scaling
Cootmodel building
MOSFLMdata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM066174
National Institutes of Health/National Institute of General Medical SciencesUnited StatesAI109764
National Institutes of Health/National Institute of General Medical SciencesUnited StatesAI081059

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Database references