4RU4

Crystal structure of the tailspike protein gp49 from Pseudomonas phage LKA1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.132 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1038/s41598-017-16411-4
  • Primary Citation of Related Structures:  
    4RU4, 4RU5

  • 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 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.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tail spike protein gp49
A, B, C, D, E
A, B, C, D, E, F
602Pseudomonas phage LKA1Mutation(s): 0 
Gene Names: gp49, PPLKA1_gp49
UniProt
Find proteins for Q0E5W5 (Pseudomonas phage LKA1)
Explore Q0E5W5 
Go to UniProtKB:  Q0E5W5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0E5W5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download Ideal Coordinates CCD File 
DA [auth C]
EA [auth C]
G [auth A]
H [auth A]
I [auth A]
DA [auth C],
EA [auth C],
G [auth A],
H [auth A],
I [auth A],
IA [auth D],
JA [auth D],
PA [auth E],
QA [auth E],
RA [auth E],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
XA [auth F],
YA [auth F],
ZA [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
AB [auth F]
CA [auth B]
HA [auth C]
NA [auth D]
OA [auth D]
AB [auth F],
CA [auth B],
HA [auth C],
NA [auth D],
OA [auth D],
Q [auth A],
R [auth A],
WA [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA
Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
FA [auth C]
GA [auth C]
J [auth A]
AA [auth B],
BA [auth B],
FA [auth C],
GA [auth C],
J [auth A],
K [auth A],
KA [auth D],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
N [auth A],
O [auth A],
P [auth A],
SA [auth E],
TA [auth E],
UA [auth E],
VA [auth E],
X [auth B],
Y [auth B],
Z [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.132 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.4α = 90
b = 148.234β = 90.85
c = 117.582γ = 90
Software Package:
Software NamePurpose
RemDAqdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Advisory, 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
  • Version 1.4: 2024-02-28
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary