5AO8

Crystal Structure of SltB3 from Pseudomonas aeruginosa in complex with NAG-NAM-pentapeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Turnover of Bacterial Cell Wall by Sltb3, a Multidomain Lytic Transglycosylase of Pseudomonas Aeruginosa.

Lee, M.Dominguez-Gil, T.Hesek, D.Mahasenan, K.V.Lastochkin, E.Hermoso, J.A.Mobashery, S.

(2016) Acs Chem.Biol. 11: 1525

  • DOI: 10.1021/acschembio.6b00194
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A family of 11 lytic transglycosylases in Pseudomonas aeruginosa, an opportunistic human pathogen, turn over the polymeric bacterial cell wall in the course of its recycling, repair, and maturation. The functions of these enzymes are not fully unders ...

    A family of 11 lytic transglycosylases in Pseudomonas aeruginosa, an opportunistic human pathogen, turn over the polymeric bacterial cell wall in the course of its recycling, repair, and maturation. The functions of these enzymes are not fully understood. We disclose herein that SltB3 of P. aeruginosa is an exolytic lytic transglycosylase. We characterize its reaction and its products by the use of peptidoglycan-based molecules. The enzyme recognizes a minimum of four sugars in its substrate but can process a substrate comprised of a peptidoglycan of 20 sugars. The ultimate product of the reaction is N-acetylglucosamine-1,6-anhydro-N-acetylmuramic acid. The X-ray structure of this enzyme is reported for the first time. The enzyme is comprised of four domains, arranged within an annular conformation. The polymeric linear peptidoglycan substrate threads through the opening of the annulus, as it experiences turnover.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Notre Dame , Nieuwland Science Hall, Notre Dame, Indiana 46556, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SOLUBLE LYTIC TRANGLYCOSILASE B3
A
420Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Find proteins for Q9HX28 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9HX28
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NM9
Query on NM9

Download SDF File 
Download CCD File 
A
(2R)-2-[(2R,3S,4R,5R,6R)-5-acetamido-2-(hydroxymethyl)-6-methoxy-3-oxidanyl-oxan-4-yl]oxypropanamide
C12 H22 N2 O7
RDTUJRBFQHDOEJ-PKKPQKKZSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 111.101α = 90.00
b = 61.440β = 90.00
c = 49.870γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 2.0: 2018-08-22
    Type: Advisory, Atomic model, Data collection, Derived calculations