4OK7

Structure of bacteriophage SPN1S endolysin from Salmonella typhimurium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


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

  • 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 glycosid ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endolysin
A, B, C
223Salmonella phage SPN1SN/A
Find proteins for H2D0G4 (Salmonella phage SPN1S)
Go to UniProtKB:  H2D0G4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 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 = 90.00
b = 120.597β = 90.00
c = 126.474γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data collection
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data reduction
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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