Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 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 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.99 kDa 
• Atom Count: 1846 
• Modelled Residue Count: 220 
• Deposited Residue Count: 248 
• Unique protein chains: 1

5WLY

E. coli LpxH- 8 mutations

• PDB DOI: 10.2210/pdb5WLY/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-07-28 Released: 2018-04-11 
• Deposition Author(s): Bohl, T.E., Aihara, H., Shi, K., Lee, J.K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.227 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

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

• PubMed: 29626094 
• DOI: 10.1074/jbc.RA118.002503
• Primary Citation of Related Structures:  
  5WLY


• 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 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 MS 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.

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Organizational Affiliation: 

From the Department of Biochemistry, Molecular Biology & Biophysics and [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-2,3-diacylglucosamine hydrolase	A	248	Escherichia coli	Mutation(s): 8  Gene Names: lpxH, AUQ13_20415, BK337_17315, BUE81_23120, EC3234A_5c00260, PGD_02789 EC: 3.6.1.54
UniProt
Find proteins for P43341 (Escherichia coli (strain K12)) Explore P43341  Go to UniProtKB:  P43341

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
FMT	E [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.227 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.012	α = 90
b = 62.064	β = 90
c = 66.047	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
Aimless	data scaling
PHENIX	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-07-28 
• Released Date: 2018-04-11 
Deposition Author(s): Bohl, T.E., Aihara, H., Shi, K., Lee, J.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118047
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41-GM103403
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357

Revision History  

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