4FET

Catalytic domain of germination-specific lytic tansglycosylase SleB from Bacillus anthracis

• PDB DOI: https://doi.org/10.2210/pdb4FET/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus anthracis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-05-30 Released: 2012-07-25 
• Deposition Author(s): Jing, X., Heffron, J., Popham, D.L., Schubot, F.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.249 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6TCI

Literature

The catalytic domain of the germination-specific lytic transglycosylase SleB from Bacillus anthracis displays a unique active site topology.

Jing, X., Robinson, H.R., Heffron, J.D., Popham, D.L., Schubot, F.D.

(2012) Proteins 80: 2469-2475

• PubMed: 22777830 
• DOI: https://doi.org/10.1002/prot.24140
• Primary Citation of Related Structures:  
  4FET


• PubMed Abstract: 
  

  Bacillus anthracis produces metabolically inactive spores. Germination of these spores requires germination-specific lytic enzymes (GSLEs) that degrade the unique cortex peptidoglycan to permit resumption of metabolic activity and outgrowth. We report the first crystal structure of the catalytic domain of a GSLE, SleB. The structure revealed a transglycosylase fold with unique active site topology and permitted identification of the catalytic glutamate residue. Moreover, the structure provided insights into the molecular basis for the specificity of the enzyme for muramic-δ-lactam-containing cortex peptidoglycan. The protein also contains a metal-binding site that is positioned directly at the entrance of the substrate-binding cleft.

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Organizational Affiliation: 

Virginia Tech, Department of Biological Sciences, Life Sciences, Blacksburg, Virginia 24061, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.79 kDa 
• Atom Count: 2,146 
• Modelled Residue Count: 245 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spore cortex-lytic enzyme prepeptide	A [auth B], B [auth A]	222	Bacillus anthracis	Mutation(s): 1  Gene Names: sleB, BA_2748, BAS2562, GBAA_2748
UniProt
Find proteins for A0A6L8PLE1 (Bacillus anthracis) Explore A0A6L8PLE1  Go to UniProtKB:  A0A6L8PLE1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth B], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth B], B [auth A]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.249 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.85	α = 90
b = 64.45	β = 90
c = 84.02	γ = 90

Software Package:

Software Name	Purpose
CCP4	refinement
PHENIX	model building
REFMAC	refinement
CCP4	data reduction
CCP4	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-25 
Deposition Author(s): Jing, X., Heffron, J., Popham, D.L., Schubot, F.D.

Revision History  

• Version 1.0: 2012-07-25
  Type: Initial release
  
• Version 1.1: 2012-09-26
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description