4KRU

X-ray structure of catalytic domain of endolysin from clostridium perfringens phage phiSM101


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report



Literature

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: 10.1111/mmi.12559
  • Structures With Same Primary Citation

  • 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 ho ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Autolytic lysozymeA229Clostridium phage phiSM101Mutation(s): 0 
Gene Names: CPR_C0050
EC: 3.2.1.17
Find proteins for Q0SPG7 (Clostridium phage phiSM101)
Explore Q0SPG7 
Go to UniProtKB:  Q0SPG7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download CCD File 
A
2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.77α = 90
b = 57.62β = 90
c = 73.42γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary