5MPQ | pdb_00005mpq

Bulgecin A: The key to a broad-spectrum inhibitor that targets lytic transglycosylases

• PDB DOI: https://doi.org/10.2210/pdb5MPQ/pdb

• Classification: LYASE
• Organism(s): Neisseria meningitidis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-17 Released: 2017-03-29 
• Deposition Author(s): Williams, A.H.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.270 (DCC) 

Starting Model: experimental

Literature

Bulgecin A: The Key to a Broad-Spectrum Inhibitor That Targets Lytic Transglycosylases.

Williams, A.H., Wheeler, R., Thiriau, C., Haouz, A., Taha, M.K., Boneca, I.G.

(2017) Antibiotics (Basel) 6

• PubMed: 28241458 
• DOI: https://doi.org/10.3390/antibiotics6010008
• Primary Citation Related Structures: 
  5MPQ


• PubMed Abstract: 
  

  Lytic transglycosylases (Lts) are involved in recycling, cell division, and metabolism of the peptidoglycan. They have been understudied for their usefulness as potential antibacterial targets due to their high redundancy in Gram-negative bacteria. Bulgecin A is an O-sulphonated glycopeptide that targets primarily soluble lytic tranglycosylases (Slt). It has been shown that bulgecin A increases the efficacy of β-lactams that target penicillin bindings proteins (PBPs). Here, we present the high-resolution crystal structure of LtgA from Neisseria meningitidis strain MC58, a membrane bound homolog of Escherichia coli Slt, in complex with bulgecin A. The LtgA-bulgecin A complex reveals the mechanism of inhibition by bulgecin A at near atomic resolution. We further demonstrate that bulgecin A is not only a potent inhibitor of LtgA, but most importantly, it restores the efficacy of β-lactam antibiotics in strains of N. meningitidis and Neisseria gonorrhoeae that have reduced susceptibility to β-lactams. This is particularly relevant for N. gonorrhoeae where no vaccines are available. This work illustrates how best to target dangerous pathogens using a multiple drug target approach, a new and alternative approach to fighting antibiotic resistance.

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Organizational Affiliation: 
• Institut Pasteur, Unité Biologie et génétique de la paroi bactérienne, Dept. Microbiologie, 28 Rue du Dr. Roux, 75015 Paris, France. [e-mail].
Institut National de la santé et de la Recherche Médicale (INSERM), Groupe Avenir, 75015 Paris, France. [e-mail].
Institut Pasteur, Unité Biologie et génétique de la paroi bactérienne, Dept. Microbiologie, 28 Rue du Dr. Roux, 75015 Paris, France. [e-mail].
Institut National de la santé et de la Recherche Médicale (INSERM), Groupe Avenir, 75015 Paris, France. [e-mail].
Institut Pasteur, Unité Biologie et génétique de la paroi bactérienne, Dept. Microbiologie, 28 Rue du Dr. Roux, 75015 Paris, France. [e-mail].
Institut National de la santé et de la Recherche Médicale (INSERM), Groupe Avenir, 75015 Paris, France. [e-mail].
Institut Pasteur, CNRS-UMR3528, Plate-forme de Cristallographie, 25 Rue Dr. Roux, 75724 Paris, France. [e-mail].
Institut Pasteur, Unité des Infection Bactériennes Invasives, Dept. Infection et Epidémiologie, 28 Rue du Dr. Roux, 75015 Paris, France. [e-mail].
Institut Pasteur, Unité Biologie et génétique de la paroi bactérienne, Dept. Microbiologie, 28 Rue du Dr. Roux, 75015 Paris, France. [e-mail].
Institut National de la santé et de la Recherche Médicale (INSERM), Groupe Avenir, 75015 Paris, France. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.54 kDa 
• Atom Count: 4,948 
• Modeled Residue Count: 576 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transglycosylase	A	576	Neisseria meningitidis	Mutation(s): 0  Gene Names: slt, ERS514729_01258 EC: 4.2.2
UniProt
Find proteins for Q9JXP1 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q9JXP1  Go to UniProtKB:  Q9JXP1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BLG	B [auth A]	4-O-(4-O-SULFONYL-N-ACETYLGLUCOSAMININYL)-5-METHYLHYDROXY-L-PROLINE-TAURINE C16 H30 N3 O14 S2 RPNZWZDLNYCCIG-HMMVDTEZSA-O
NHE	E [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.270 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.834	α = 90
b = 71.561	β = 90
c = 121.123	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Williams, A.H.

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Funding Organization	Location	Grant Number
European Research Council	France	202283

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2017-05-10
  Changes: Database references
• Version 1.2: 2017-05-17
  Changes: Database references
• Version 1.3: 2024-01-17
  Changes: Author supporting evidence, Data collection, Database references, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary