4OK7

Structure of bacteriophage SPN1S endolysin from Salmonella typhimurium

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.208 

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This is version 1.2 of the entry. See complete history. 


Literature

Structure of bacteriophage SPN1S endolysin reveals an unusual two-module fold for the peptidoglycan lytic and binding activity.

Park, Y., Lim, J.A., Kong, M., Ryu, S., Rhee, S.

(2014) Mol Microbiol 92: 316-325

  • DOI: 10.1111/mmi.12555
  • Primary Citation of Related Structures:  
    4OK7

  • PubMed Abstract: 

    • Bacteriophage SPN1S infects the pathogenic Gram-negative bacterium Salmonella typhimurium and expresses endolysin for the release of phage progeny by degrading peptidoglycan of the host cell walls. Bacteriophage SPN1S endolysin exhibits high glycosidase activity against peptidoglycans, resulting in antimicrobial activity against a broad range of outer membrane-permeabilized Gram-negative bacteria ...

    Bacteriophage SPN1S infects the pathogenic Gram-negative bacterium Salmonella typhimurium and expresses endolysin for the release of phage progeny by degrading peptidoglycan of the host cell walls. Bacteriophage SPN1S endolysin exhibits high glycosidase activity against peptidoglycans, resulting in antimicrobial activity against a broad range of outer membrane-permeabilized Gram-negative bacteria. Here, we report a crystal structure of SPN1S endolysin, indicating that unlike most endolysins from Gram-negative bacteria background, the α-helical protein consists of two modular domains, a large and a small domain, with a concave groove between them. Comparison with other structurally homologous glycoside hydrolases indicated a possible peptidoglycan binding site in the groove, and the presence of a catalytic dyad in the vicinity of the groove, one residue in a large domain and the other in a junction between the two domains. The catalytic dyad was further validated by antimicrobial activity assay against outer membrane-permeabilized Escherichia coli. The three-helix bundle in the small domain containing a novel class of sequence motif exhibited binding affinity against outer membrane-permeabilized E. coli and was therefore proposed as the peptidoglycan-binding domain. These structural and functional features suggest that endolysin from a Gram-negative bacterial background has peptidoglycan-binding activity and performs glycoside hydrolase activity through the catalytic dyad.

    Organizational Affiliation: 

    Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EndolysinA, B, C223Salmonella phage SPN1SMutation(s): 0 
Gene Names: SPC32N_026, SPN1S_0028
UniProt
Find proteins for H2D0G4 (Salmonella phage SPN1S)
Explore H2D0G4 
Go to UniProtKB:  H2D0G4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH2D0G4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth B],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
U [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
O [auth B],
P [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.616α = 90
b = 120.597β = 90
c = 126.474γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-04-30
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description