5V8E | pdb_00005v8e

Structure of Bacillus cereus PatB1

• PDB DOI: https://doi.org/10.2210/pdb5V8E/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Bacillus cereus ATCC 10987
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-03-21 Released: 2017-10-18 
• Deposition Author(s): Sychantha, D., Little, D.J., Chapman, R.N., Boons, G.J., Robinson, H., Howell, P.L., Clarke, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.241 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

PatB1 is an O-acetyltransferase that decorates secondary cell wall polysaccharides.

Sychantha, D., Little, D.J., Chapman, R.N., Boons, G.J., Robinson, H., Howell, P.L., Clarke, A.J.

(2018) Nat Chem Biol 14: 79-85

• PubMed: 29083419 
• DOI: https://doi.org/10.1038/nchembio.2509
• Primary Citation Related Structures: 
  5V8D, 5V8E


• PubMed Abstract: 
  

  O-Acetylation of the secondary cell wall polysaccharides (SCWP) of the Bacillus cereus group of pathogens, which includes Bacillus anthracis, is essential for the proper attachment of surface-layer (S-layer) proteins to their cell walls. Using a variety of pseudosubstrates and a chemically synthesized analog of SCWP, we report here the identification of PatB1 as a SCWP O-acetyltransferase in Bacillus cereus. Additionally, we report the crystal structure of PatB1, which provides detailed insights into the mechanism of this enzyme and defines a novel subfamily of the SGNH family of esterases and lipases. We propose a model for the O-acetylation of SCWP requiring the translocation of acetyl groups from a cytoplasmic source across the plasma membrane by PatA1 and PatA2 for their transfer to SCWP by PatB1.

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Organizational Affiliation: 
• Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
Program in Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada.
Department of Biochemistry, University of Toronto, Ontario, Canada.
Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
Photon Science Division, Brookhaven National Laboratory, Upton, New York, 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 Evidence: gel filtration

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: 72.53 kDa 
• Atom Count: 5,130 
• Modeled Residue Count: 610 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacillus cereus PatB1	A, B	309	Bacillus cereus ATCC 10987	Mutation(s): 6  Gene Names: BCE_0974
UniProt
Find proteins for Q73CU0 (Bacillus cereus (strain ATCC 10987 / NRS 248)) Explore Q73CU0  Go to UniProtKB:  Q73CU0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], D [auth A], H [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
PEG	F [auth A], G [auth A], I [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.241 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.76	α = 90
b = 133.76	β = 90
c = 87.311	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHASER	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-18 
Deposition Author(s): Sychantha, D., Little, D.J., Chapman, R.N., Boons, G.J., Robinson, H., Howell, P.L., Clarke, A.J.

Revision History  

• Version 1.0: 2017-10-18
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Database references
• Version 1.2: 2017-12-20
  Changes: Database references
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Structure summary