Lytic transglycosylase in action

Experimental Data Snapshot

  • Resolution: 1.43 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1074/jbc.RA117.001095
  • Primary Citation of Related Structures:  
    5O1J, 5O24, 5O29, 5O2N, 6FPN

  • 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 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

    From the Institut Pasteur, Département de Microbiologie, Unité Biologie et Génétique de la Paroi Bactérienne, 75015 Paris, France, awilliam@pasteur.fr.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transglycosylase590Neisseria meningitidisMutation(s): 0 
Gene Names: sltERS514729_01258
EC: 4.2.2
Find proteins for Q9JXP1 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q9JXP1 
Go to UniProtKB:  Q9JXP1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JXP1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.43 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.714α = 90
b = 72.681β = 90
c = 124.924γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-05-02
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-28
    Changes: Data collection, Structure summary
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description