4RU5 | pdb_00004ru5

Crystal Structure of the Pseudomonas phage phi297 tailspike gp61

• PDB DOI: https://doi.org/10.2210/pdb4RU5/pdb

• Classification: LYASE
• Organism(s): Pseudomonas phage phi297
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-18 Released: 2015-11-18 
• Deposition Author(s): Browning, C., Sycheva, L.V., Shneider, M.M., Leiman, P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.120 (Depositor), 0.119 (DCC) 
• R-Value Work: 
  0.079 (Depositor), 0.079 (DCC) 
• R-Value Observed: 
  0.081 (Depositor) 

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

• PubMed: 29176754 
• DOI: https://doi.org/10.1038/s41598-017-16411-4
• Primary Citation 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.

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Organizational Affiliation: 
• Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw, 51-148, Poland.
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, Galveston, TX, 77555-0647, USA.
Vertex Pharmaceuticals (Europe) Ltd, Abingdon, Oxfordshire, OX14 4RW, UK.
Affinivax Inc., Cambridge, 02139-3543, Massachusetts, USA.
Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium.
N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russia.
Department of Biochemistry and Genetics, Institute of Biology, The Jan Kochanowski University in Kielce, Kielce, 25-406, Poland.
Department of Molecular Physics, Institute of Physics, The Jan Kochanowski University in Kielce, Kielce, 25-406, Poland.
Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw, 51-148, Poland. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 194.51 kDa 
• Atom Count: 17,240 
• Modeled Residue Count: 1,802 
• Deposited Residue Count: 1,815 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tailspike gp27	A, B, C	605	Pseudomonas phage phi297	Mutation(s): 0  Gene Names: phi297_00061
UniProt
Find proteins for A0ACD6B8L6 (Pseudomonas phage phi297) Explore A0ACD6B8L6  Go to UniProtKB:  A0ACD6B8L6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth C], JA [auth C], L [auth A], M [auth A], N [auth A], O [auth A], U [auth B], V [auth B], W [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	KA [auth C], LA [auth C], MA [auth C], P [auth A], X [auth B], Y [auth B], Z [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	AA [auth C], BA [auth C], D [auth A], E [auth A], Q [auth B], R [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	CA [auth C], DA [auth C], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], S [auth B], T [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.120 (Depositor), 0.119 (DCC) 
• R-Value Work:  0.079 (Depositor), 0.079 (DCC) 
• R-Value Observed: 0.081 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 210.617	α = 90
b = 124.705	β = 97.93
c = 83.563	γ = 90

Software Package:

Software Name	Purpose
RemDAq	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Browning, C., Sycheva, L.V., Shneider, M.M., Leiman, P.G.

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
• Version 1.4: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary