4RU5

Crystal Structure of the Pseudomonas phage phi297 tailspike gp61


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.120 
  • R-Value Work: 0.079 
  • R-Value Observed: 0.081 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The O-specific polysaccharide lyase from the phage LKA1 tailspike reduces Pseudomonas virulence.

Olszak, T.Shneider, M.M.Latka, A.Maciejewska, B.Browning, C.Sycheva, L.V.Cornelissen, A.Danis-Wlodarczyk, K.Senchenkova, S.N.Shashkov, A.S.Gula, G.Arabski, M.Wasik, S.Miroshnikov, K.A.Lavigne, R.Leiman, P.G.Knirel, Y.A.Drulis-Kawa, Z.

(2017) Sci Rep 7: 16302-16302

  • DOI: 10.1038/s41598-017-16411-4
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Pseudomonas phage LKA1 of the subfamily Autographivirinae encodes a tailspike protein (LKA1gp49) which binds and cleaves B-band LPS (O-specific antigen, OSA) of Pseudomonas aeruginosa PAO1. The crystal structure of LKA1gp49 catalytic domain consists ...

    Pseudomonas phage LKA1 of the subfamily Autographivirinae encodes a tailspike protein (LKA1gp49) which binds and cleaves B-band LPS (O-specific antigen, OSA) of Pseudomonas aeruginosa PAO1. The crystal structure of LKA1gp49 catalytic domain consists of a beta-helix, an insertion domain and a C-terminal discoidin-like domain. The putative substrate binding and processing site is located on the face of the beta-helix whereas the C-terminal domain is likely involved in carbohydrates binding. NMR spectroscopy and mass spectrometry analyses of degraded LPS (OSA) fragments show an O5 serotype-specific polysaccharide lyase specificity. LKA1gp49 reduces virulence in an in vivo Galleria mellonella infection model and sensitizes P. aeruginosa to serum complement activity. This enzyme causes biofilm degradation and does not affect the activity of ciprofloxacin and gentamicin. This is the first comprehensive report on LPS-degrading lyase derived from a Pseudomonas phage. Biological properties reveal a potential towards its applications in antimicrobial design and as a microbiological or biotechnological tool.


    Organizational Affiliation

    Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw, 51-148, Poland. zuzanna.drulis-kawa@uwr.edu.pl.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tailspike gp27
A, B, C
605Pseudomonas phage phi297Mutation(s): 0 
Gene Names: phi297_00061
Find proteins for H2BD96 (Pseudomonas phage phi297)
Go to UniProtKB:  H2BD96
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download CCD File 
A, B, C
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A, B, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.120 
  • R-Value Work: 0.079 
  • R-Value Observed: 0.081 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.617α = 90
b = 124.705β = 97.93
c = 83.563γ = 90
Software Package:
Software NamePurpose
RemDAqdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2018-02-21
    Changes: Database references
  • Version 1.3: 2018-04-18
    Changes: Data collection, Database references, Derived calculations, Structure summary