6FBT

The X-ray Structure of Lytic Transglycosylase Slt from Pseudomonas aeruginosa in complex with the reaction product NAG-anhNAMpentapeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Exolytic and endolytic turnover of peptidoglycan by lytic transglycosylase Slt ofPseudomonas aeruginosa.

Lee, M.Batuecas, M.T.Tomoshige, S.Dominguez-Gil, T.Mahasenan, K.V.Dik, D.A.Hesek, D.Millan, C.Uson, I.Lastochkin, E.Hermoso, J.A.Mobashery, S.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 4393-4398

  • DOI: 10.1073/pnas.1801298115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • β-Lactam antibiotics inhibit cell-wall transpeptidases, preventing the peptidoglycan, the major constituent of the bacterial cell wall, from cross-linking. This causes accumulation of long non-cross-linked strands of peptidoglycan, which leads to bac ...

    β-Lactam antibiotics inhibit cell-wall transpeptidases, preventing the peptidoglycan, the major constituent of the bacterial cell wall, from cross-linking. This causes accumulation of long non-cross-linked strands of peptidoglycan, which leads to bacterial death. Pseudomonas aeruginosa , a nefarious bacterial pathogen, attempts to repair this aberrantly formed peptidoglycan by the function of the lytic transglycosylase Slt. We document in this report that Slt turns over the peptidoglycan by both exolytic and endolytic reactions, which cause glycosidic bond scission from a terminus or in the middle of the peptidoglycan, respectively. These reactions were characterized with complex synthetic peptidoglycan fragments that ranged in size from tetrasaccharides to octasaccharides. The X-ray structure of the wild-type apo Slt revealed it to be a doughnut-shaped protein. In a series of six additional X-ray crystal structures, we provide insights with authentic substrates into how Slt is enabled for catalysis for both the endolytic and exolytic reactions. The substrate for the exolytic reaction binds Slt in a canonical arrangement and reveals how both the glycan chain and the peptide stems are recognized by the Slt. We document that the apo enzyme does not have a fully formed active site for the endolytic reaction. However, binding of the peptidoglycan at the existing subsites within the catalytic domain causes a conformational change in the protein that assembles the surface for binding of a more expansive peptidoglycan between the catalytic domain and an adjacent domain. The complexes of Slt with synthetic peptidoglycan substrates provide an unprecedented snapshot of the endolytic reaction.


    Organizational Affiliation

    Structural Biology Unit, Institute of Molecular Biology of Barcelona, Consejo Superior de Investigaciones Científicas, E-08028 Barcelona, Spain.,Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, E-28006 Madrid, Spain; xjuan@iqfr.csic.es mobashery@nd.edu.,Structural Biology Unit, Institució Catalana de Recerca i Estudis Avançats, E-08003 Barcelona, Spain.,Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556.,Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, E-28006 Madrid, Spain.,Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556; xjuan@iqfr.csic.es mobashery@nd.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lytic murein transglycosylase
A
610Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Find proteins for Q9HZI6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9HZI6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NAG-anhNAMpentapeptide
E
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
API
Query on API
E
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
AH0
Query on AH0
E
NON-POLYMERC11 H17 N O7

--

DGL
Query on DGL
E
D-PEPTIDE LINKINGC5 H9 N O4

--

DAL
Query on DAL
E
D-PEPTIDE LINKINGC3 H7 N O2

--

NAG
Query on NAG
E
D-SACCHARIDEC8 H15 N O6

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.180 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 165.526α = 90.00
b = 165.526β = 90.00
c = 54.733γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesAI104987

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-05-02
    Type: Data collection, Database references