5WLY

E. coli LpxH- 8 mutations

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release.

Bohl, T.E., Ieong, P., Lee, J.K., Lee, T., Kankanala, J., Shi, K., Demir, O., Kurahashi, K., Amaro, R.E., Wang, Z., Aihara, H.

(2018) J. Biol. Chem. 293: 7969-7981

  • DOI: 10.1074/jbc.RA118.002503

  • PubMed Abstract: 

    • Gram-negative bacteria are surrounded by a secondary membrane of which the outer leaflet is composed of the glycolipid lipopolysaccharide (LPS), which guards against hydrophobic toxins, including many antibiotics. Therefore, LPS synthesis in bacteria ...

    Gram-negative bacteria are surrounded by a secondary membrane of which the outer leaflet is composed of the glycolipid lipopolysaccharide (LPS), which guards against hydrophobic toxins, including many antibiotics. Therefore, LPS synthesis in bacteria is an attractive target for antibiotic development. LpxH is a pyrophosphatase involved in LPS synthesis, and previous structures revealed that LpxH has a helical cap that binds its lipid substrates. Here, crystallography and hydrogen-deuterium exchange mass spectrometry provided evidence for a highly flexible substrate-binding cap in LpxH. Furthermore, molecular dynamics simulations disclosed how the helices of the cap may open to allow substrate entry. The predicted opening mechanism was supported by activity assays of LpxH variants. Finally, we confirmed biochemically that LpxH is inhibited by a previously identified antibacterial compound, determined the potency of this inhibitor, and modeled its binding mode in the LpxH active site. In summary, our work provides evidence that the substrate-binding cap of LpxH is highly dynamic thus allowing for facile substrate binding and product release between the capping helices. Our results also pave the way for the rational design of more potent LpxH inhibitors.

    Organizational Affiliation: 

    Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota: Twin Cities, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-2,3-diacylglucosamine hydrolase
A
248Escherichia coli (strain K12)Mutation(s): 8 
Gene Names: lpxH (ybbF)
EC: 3.6.1.54
Find proteins for P43341 (Escherichia coli (strain K12))
Go to UniProtKB:  P43341
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN
Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT
Download SDF File 
Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO
Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.198 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 57.012α = 90.00
b = 62.064β = 90.00
c = 66.047γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHENIXphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118047
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41-GM103403
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History 

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references
  • Version 1.2: 2018-06-06
    Type: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2018-07-11
    Type: Data collection, Structure summary
  • Version 1.4: 2020-01-01
    Type: Author supporting evidence