6FCS

The X-ray Structure of Lytic Transglycosylase Slt inactive mutant E503Q from Pseudomonas aeruginosa in complex with NAG-NAMpentapeptide-NAG-NAMpentapeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 

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
  • Structures With Same Primary Citation

  • 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

    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
Soluble lytic murein transglycosylase
A
613Pseudomonas aeruginosaMutation(s): 1 
Gene Names: sltAOY09_04369PAMH19_2049E4V10_02545IPC1481_13125IPC1509_14880
EC: 4.2.2
Find proteins for A0A069QJX4 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A069QJX4
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALA-DGL-API-DAL-DAL
B
5Pseudomonas aeruginosaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMV
Query on AMV

Download CCD File 
B
METHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSIDE
C12 H21 N O8
UXEQYDNCHCKBIL-PKKPQKKZSA-N
 Ligand Interaction
AMU
Query on AMU

Download CCD File 
A
BETA-N-ACETYLMURAMIC ACID
C11 H19 N O8
MNLRQHMNZILYPY-YVNCZSHWSA-N
 Ligand Interaction
NM6
Query on NM6

Download CCD File 
B
(2R)-2-[(2R,3S,4R,5R,6R)-5-acetamido-2-(hydroxymethyl)-3,6-bis(oxidanyl)oxan-4-yl]oxypropanamide
C11 H20 N2 O7
MLHXTMGNPGMLSD-YVNCZSHWSA-N
 Ligand Interaction
MAG
Query on MAG

Download CCD File 
A
BETA-METHYL-N-ACETYL-D-GLUCOSAMINE
C9 H17 N O6
ZEVOCXOZYFLVKN-JGKVKWKGSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
66N
Query on 66N

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A
L-alaninamide
C3 H8 N2 O
HQMLIDZJXVVKCW-REOHCLBHSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
API
Query on API
B
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.873α = 90
b = 166.873β = 90
c = 54.509γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
    Changes: Data collection, Database references