5JIP

Crystal structure of the Clostridium perfringens spore cortex lytic enzyme SleM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

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This is version 1.3 of the entry. See complete history


Literature

The crystal structure of Clostridium perfringens SleM, a muramidase involved in cortical hydrolysis during spore germination.

Al-Riyami, B.Ustok, F.I.Stott, K.Chirgadze, D.Y.Christie, G.

(2016) Proteins 84: 1681-1689

  • DOI: https://doi.org/10.1002/prot.25112
  • Primary Citation of Related Structures:  
    5JIP

  • PubMed Abstract: 

    Clostridium perfringens spores employ two peptidoglycan lysins to degrade the spore cortex during germination. SleC initiates cortex hydrolysis to generate cortical fragments that are degraded further by the muramidase SleM. Here, we present the crystal structure of the C. perfringens S40 SleM protein at 1.8 Å. SleM comprises an N-terminal catalytic domain that adopts an irregular α/β-barrel fold that is common to GH25 family lysozymes, plus a C-terminal fibronectin type III domain. The latter is involved in forming the SleM dimer that is evident in both the crystal structure and in solution. A truncated form of SleM that lacks the FnIII domain shows reduced activity against spore sacculi indicating that this domain may have a role in facilitating the position of substrate with respect to the enzyme's active site. Proteins 2016; 84:1681-1689. © 2016 Wiley Periodicals, Inc.


  • Organizational Affiliation

    Department of Chemical Engineering and Biotechnology, Institute of Biotechnology, University of Cambridge, Cambridge, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cortical-lytic enzyme
A, B
332Clostridium perfringensMutation(s): 0 
Gene Names: sleM
UniProt
Find proteins for O06496 (Clostridium perfringens)
Explore O06496 
Go to UniProtKB:  O06496
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06496
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.599α = 90
b = 85.852β = 105.51
c = 87.205γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-08-17
    Changes: Database references
  • Version 1.2: 2016-11-02
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description