6B8B

E. coli LptB in complex with ADP and a novobiocin derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    6B8B, 6B89

  • 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 presence of the lipopolysaccharide-containing outer membrane, which acts as a permeability barrier ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lipopolysaccharide export system ATP-binding protein LptBA249Escherichia coli K-12Mutation(s): 0 
Gene Names: lptByhbGb3201JW3168
EC: 3.6.3 (PDB Primary Data), 7.5.2 (UniProt)
Find proteins for P0A9V1 (Escherichia coli (strain K12))
Explore P0A9V1 
Go to UniProtKB:  P0A9V1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CZJ
Query on CZJ

Download Ideal Coordinates CCD File 
C [auth A](3s,5s,7s)-N-{7-[(3-O-carbamoyl-6-deoxy-5-methyl-4-O-methyl-beta-D-gulopyranosyl)oxy]-4-hydroxy-8-methyl-2-oxo-2H-1-ben zopyran-3-yl}tricyclo[3.3.1.1~3,7~]decane-1-carboxamide
C30 H38 N2 O10
SFCPIJFPMNEBLW-GGTPUZHSSA-N
 Ligand Interaction
ADP
Query on ADP

Download Ideal Coordinates CCD File 
D [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.03α = 90
b = 34.78β = 101.38
c = 62.71γ = 90
Software Package:
Software NamePurpose
MOSFLMdata collection
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM066174
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesAI109764
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesAI081059

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-13
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2021-01-06
    Changes: Derived calculations, Structure summary