6P2T

BshB from Bacillus subtilis complexed with citrate

• PDB DOI: https://doi.org/10.2210/pdb6P2T/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-22 Released: 2020-01-08 
• Deposition Author(s): Cook, P.D., Meloche, C.E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.205 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Literature

X-ray crystallographic structure of BshB, the zinc-dependent deacetylase involved in bacillithiol biosynthesis.

Woodward, R.L., Castleman, M.M., Meloche, C.E., Karpen, M.E., Carlson, C.G., Yobi, W.H., Jepsen, J.C., Lewis, B.W., Zarnosky, B.N., Cook, P.D.

(2020) Protein Sci 29: 1035-1039

• PubMed: 31867856 
• DOI: https://doi.org/10.1002/pro.3808
• Primary Citation of Related Structures:  
  6P2T, 6ULL


• PubMed Abstract: 
  

  Many gram-positive bacteria produce bacillithiol to aid in the maintenance of redox homeostasis and degradation of toxic compounds, including the antibiotic fosfomycin. Bacillithiol is produced via a three-enzyme pathway that includes the action of the zinc-dependent deacetylase BshB. Previous studies identified conserved aspartate and histidine residues within the active site that are involved in metal binding and catalysis, but the enzymatic mechanism is not fully understood. Here we report two X-ray crystallographic structures of BshB from Bacillus subtilis that provide insight into the BshB catalytic mechanism.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Mount Union, Alliance, Ohio.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 29.16 kDa 
• Atom Count: 2,042 
• Modelled Residue Count: 232 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetyl-alpha-D-glucosaminyl L-malate deacetylase 1	A	256	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: bshB1, jojG, ypjG, BSU22470 EC: 3.5.1
UniProt
Find proteins for P42981 (Bacillus subtilis (strain 168)) Explore P42981  Go to UniProtKB:  P42981

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT (Subject of Investigation/LOI)	C [auth A], D [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.205 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.538	α = 90
b = 98.538	β = 90
c = 184.877	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-08 
Deposition Author(s): Cook, P.D., Meloche, C.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2020-01-08
  Type: Initial release
  
• Version 1.1: 2020-04-08
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description