5I1T

2.6 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (SpoIID) from Clostridium difficile in Complex with Triacetylchitotriose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structures of the SpoIID Lytic Transglycosylases Essential for Bacterial Sporulation.

Nocadello, S.Minasov, G.Shuvalova, L.S.Dubrovska, I.Sabini, E.Anderson, W.F.

(2016) J.Biol.Chem. 291: 14915-14926

  • DOI: 10.1074/jbc.M116.729749
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial spores are the most resistant form of life known on Earth and represent a serious problem for (i) bioterrorism attack, (ii) horizontal transmission of microbial pathogens in the community, and (iii) persistence in patients and in a nosocomi ...

    Bacterial spores are the most resistant form of life known on Earth and represent a serious problem for (i) bioterrorism attack, (ii) horizontal transmission of microbial pathogens in the community, and (iii) persistence in patients and in a nosocomial environment. Stage II sporulation protein D (SpoIID) is a lytic transglycosylase (LT) essential for sporulation. The LT superfamily is a potential drug target because it is active in essential bacterial processes involving the peptidoglycan, which is unique to bacteria. However, the absence of structural information for the sporulation-specific LT enzymes has hindered mechanistic understanding of SpoIID. Here, we report the first crystal structures with and without ligands of the SpoIID family from two community relevant spore-forming pathogens, Bacillus anthracis and Clostridium difficile. The structures allow us to visualize the overall architecture, characterize the substrate recognition model, identify critical residues, and provide the structural basis for catalysis by this new family of enzymes.


    Organizational Affiliation

    From the Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Stage II sporulation protein D
A
330Peptoclostridium difficile (strain 630)Mutation(s): 0 
Gene Names: spoIID
Find proteins for Q18CL6 (Peptoclostridium difficile (strain 630))
Go to UniProtKB:  Q18CL6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CTO
Query on CTO

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Download CCD File 
A
TRIACETYLCHITOTRIOSE
CHITOTRIOSE
C24 H41 N3 O16
WZZVUHWLNMNWLW-VFCSDQTKSA-N
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 98.082α = 90.00
b = 98.082β = 90.00
c = 108.327γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-08
    Type: Database references
  • Version 1.2: 2016-07-27
    Type: Database references