4WBD | pdb_00004wbd

The crystal structure of BshC from Bacillus subtilis complexed with citrate and ADP

• PDB DOI: https://doi.org/10.2210/pdb4WBD/pdb

• Classification: LIGASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-09-03 Released: 2014-12-31 
• Deposition Author(s): Cook, P.D., VanDuinen, A.J., Winchell, K.R.
• 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: 1.77 Å
• R-Value Free: 
  0.198 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

X-ray Crystallographic Structure of BshC, a Unique Enzyme Involved in Bacillithiol Biosynthesis.

VanDuinen, A.J., Winchell, K.R., Keithly, M.E., Cook, P.D.

(2015) Biochemistry 54: 100-103

• PubMed: 25496067 
• DOI: https://doi.org/10.1021/bi501394q
• Primary Citation of Related Structures:  
  4WBD


• PubMed Abstract: 
  

  Bacillithiol is produced by many Gram-positive bacteria via a pathway utilizing the enzymes BshA, BshB, and BshC. Here we report the 1.77 Å resolution crystal structure of BshC, the putative cysteine ligase in bacillithiol production. The structure reveals that BshC contains a core Rossmann fold with connecting peptide motifs (CP1 and CP2) and a unique α-helical coiled-coil domain that facilitates dimerization. The model contains citrate and glycerol in the canonical active site and ADP in a second binding pocket. The overall structure and bound ligands give insight into the function of this unique enzyme.

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Organizational Affiliation: 

Department of Cell & Molecular Biology, Grand Valley State University , Allendale, Michigan 49401, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 63.65 kDa 
• Atom Count: 4,645 
• Modelled Residue Count: 540 
• Deposited Residue Count: 541 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BSHC	A	541	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: yllA, BSU15120 EC: 6
UniProt
Find proteins for P55342 (Bacillus subtilis (strain 168)) Explore P55342  Go to UniProtKB:  P55342

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
CIT	C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.198 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.53	α = 90
b = 92.16	β = 116.83
c = 87.377	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-12-31 
Deposition Author(s): Cook, P.D., VanDuinen, A.J., Winchell, K.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F32GM093507
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM030910

Revision History  

• Version 1.0: 2014-12-31
  Type: Initial release
  
• Version 1.1: 2015-01-28
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Refinement description