5O24

Lytic transglycosylase in action


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.429 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 

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 metabo-lism of peptidoglycan (PG). LTs cleave the β-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) in the PG glycan stran ...

    Lytic transglycosylases (LTs) are a class of enzymes important for the recycling and metabo-lism of peptidoglycan (PG). LTs cleave the β-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) in the PG glycan strand, resulting in the concomitant formation of 1,6-anhydro-MurNAc and GlcNAc. No LTs reported to date have utilized chitins as sub-strates, despite the fact that chitins are GlcNAc pol-ymers 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 identi-fied trapped intermediates, unpredicted substrate rearrangements, sugar distortions, and a conserved crystallographic water molecule bound to the cata-lytic 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 understand-ing of the mechanisms of LTs in bacterial cell wall biology.


    Organizational Affiliation

    Institut Pasteur, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transglycosylase
A
590Neisseria 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
NHE
Query on NHE

Download SDF File 
Download CCD File 
A
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
N-CYCLOHEXYLTAURINE; CHES
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.429 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.714α = 90.00
b = 72.681β = 90.00
c = 124.924γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXphasing
PHENIXrefinement
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: 2018-05-02
    Type: Data collection, Database references
  • Version 1.2: 2018-11-28
    Type: Data collection, Structure summary