6FPN

Lytic transglycosylase in action


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A step-by-stepin crystalloguide to bond cleavage and 1,6-anhydro-sugar product synthesis by a peptidoglycan-degrading lytic transglycosylase.

Williams, A.H.Wheeler, R.Rateau, L.Malosse, C.Chamot-Rooke, J.Haouz, A.Taha, M.K.Boneca, I.G.

(2018) J. Biol. Chem. 293: 6000-6010

  • DOI: 10.1074/jbc.RA117.001095
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lytic transglycosylases (LTs) are a class of enzymes important for the recycling and metabolism of peptidoglycan (PG). LTs cleave the β-1,4-glycosidic bond between <i>N </i>-acetylmuramic acid (MurNAc) and GlcNAc in the PG glycan strand, resulting i ...

    Lytic transglycosylases (LTs) are a class of enzymes important for the recycling and metabolism of peptidoglycan (PG). LTs cleave the β-1,4-glycosidic bond between N -acetylmuramic acid (MurNAc) and GlcNAc in the PG glycan strand, resulting in the concomitant formation of 1,6-anhydro- N -acetylmuramic acid and GlcNAc. No LTs reported to date have utilized chitins as substrates, despite the fact that chitins are GlcNAc polymers linked via β-1,4-glycosidic bonds, which are the known site of chemical activity for LTs. Here, we demonstrate enzymatically that LtgA, a non-canonical, substrate-permissive LT from Neisseria meningitidis utilizes chitopentaose ((GlcNAc) 5 ) as a substrate to produce three newly identified sugars: 1,6-anhydro-chitobiose, 1,6-anhydro-chitotriose, and 1,6-anhydro-chitotetraose. Although LTs have been widely studied, their complex reactions have not previously been visualized in the crystalline state because macromolecular PG is insoluble. Here, we visualized the cleavage of the glycosidic bond and the liberation of GlcNAc-derived residues by LtgA, followed by the synthesis of atypical 1,6-anhydro-GlcNAc derivatives. In addition to the newly identified anhydro-chitin products, we identified trapped intermediates, unpredicted substrate rearrangements, sugar distortions, and a conserved crystallographic water molecule bound to the catalytic glutamate of a high-resolution native LT. This study enabled us to propose a revised alternative mechanism for LtgA that could also be applicable to other LTs. Our work contributes to the understanding of the mechanisms of LTs in bacterial cell wall biology.


    Organizational Affiliation

    the Gustave Roussy Comprehensive Cancer Center, Tumour Immunology and Immunotherapy, F-94805 Villejuif, France.,the Institut Pasteur, Plate-forme de Cristallographie, CNRS-UMR3528, 75724 Paris, France, and.,the Institut Pasteur, Département d'Infection et Epidémiologie, Unité des Infection Bactériennes Invasives, 75015 Paris, France.,INSERM, 75015 Paris, France.,From the Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 75015 Paris, France, awilliam@pasteur.fr.,From the Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 75015 Paris, France, bonecai@pasteur.fr.,From the Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 75015 Paris, France.,the Institut Pasteur, CNRS USR 2000, Unité des Spectrométrie de Masse Structurale et Proteomique, 75015 Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative soluble lytic murein transglycosylase
B
586Neisseria meningitidis serogroup B (strain MC58)Mutation(s): 0 
Find proteins for Q9JXP1 (Neisseria meningitidis serogroup B (strain MC58))
Go to UniProtKB:  Q9JXP1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.048α = 90.00
b = 72.966β = 90.00
c = 124.605γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references
  • Version 1.2: 2018-11-28
    Type: Data collection, Structure summary