X-ray structure of endolysin from clostridium perfringens phage phiSM101

Experimental Data Snapshot

  • Resolution: 1.92 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


X-ray structure of a novel endolysin encoded by episomal phage phiSM101 of Clostridium perfringens.

Tamai, E.Yoshida, H.Sekiya, H.Nariya, H.Miyata, S.Okabe, A.Kuwahara, T.Maki, J.Kamitori, S.

(2014) Mol Microbiol 92: 326-337

  • DOI: https://doi.org/10.1111/mmi.12559
  • Primary Citation of Related Structures:  
    4KRT, 4KRU

  • PubMed Abstract: 

    Gram-positive bacteria possess a thick cell wall composed of a mesh polymer of peptidoglycans, which provides physical protection. Endolysins encoded by phages infecting bacteria can hydrolyse peptidoglycans in the bacterial cell wall, killing the host bacteria immediately. The endolysin (Psm) encoded by episomal phage phiSM101 of enterotoxigenic Clostridium perfringens type A strain SM101 exhibits potent lytic activity towards most strains of Clostridium perfringens. Psm has an N-terminal catalytic domain highly homologous to N-acetylmuramidases belonging to the glycoside hydrolase 25 family, and C-terminal tandem repeated bacterial Src homology 3 (SH3_3) domains as the cell wall-binding domain. The X-ray structure of full-length Psm and a catalytic domain of Psm in complex with N-acetylglucosamine were determined to elucidate the catalytic reaction and cell wall recognition mechanisms of Psm. The results showed that Psm may have adopted a neighbouring-group mechanism for the catalytic hydrolysing reaction in which the N-acetyl carbonyl group of the substrate was involved in the formation of an oxazolinium ion intermediate. Based on structural comparisons with other endolysins and a modelling study, we proposed that tandem repeated SH3_3 domains of Psm recognized the peptide side-chains of peptidoglycans to assist the catalytic domain hydrolysing the glycan backbone.

  • Organizational Affiliation

    Life Science Research Center, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan; Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Autolytic lysozyme
A, B
353Clostridium phage phiSM101Mutation(s): 0 
Gene Names: CPR_C0050
Find proteins for Q0SPG7 (Clostridium phage phiSM101)
Explore Q0SPG7 
Go to UniProtKB:  Q0SPG7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0SPG7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EPE

Download Ideal Coordinates CCD File 
C8 H18 N2 O4 S
Query on MLA

Download Ideal Coordinates CCD File 
E [auth A],
P [auth B]
C3 H4 O4
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
D [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
Q [auth B],
R [auth B],
S [auth B]
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.92 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.6α = 90
b = 112.9β = 91.35
c = 64.95γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2015-04-29
    Changes: Non-polymer description
  • Version 1.2: 2019-12-18
    Changes: Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description