5D00

Crystal structure of BshA from B. subtilis complexed with N-acetylglucosaminyl-malate and UMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A Structural, Functional, and Computational Analysis of BshA, the First Enzyme in the Bacillithiol Biosynthesis Pathway.

Winchell, K.R.Egeler, P.W.VanDuinen, A.J.Jackson, L.B.Karpen, M.E.Cook, P.D.

(2016) Biochemistry 55: 4654-4665

  • DOI: 10.1021/acs.biochem.6b00472
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Bacillithiol is a compound produced by several Gram-positive bacterial species, including the human pathogens Staphylococcus aureus and Bacillus anthracis. It is involved in maintaining cellular redox balance as well as the destruction of reactive ox ...

    Bacillithiol is a compound produced by several Gram-positive bacterial species, including the human pathogens Staphylococcus aureus and Bacillus anthracis. It is involved in maintaining cellular redox balance as well as the destruction of reactive oxygen species and harmful xenobiotic agents, including the antibiotic fosfomycin. BshA, BshB, and BshC are the enzymes involved in bacillithiol biosynthesis. BshA is a retaining glycosyltransferase responsible for the first committed step in bacillithiol production, namely the addition of N-acetylglucosamine to l-malate. Retaining glycosyltransferases like BshA are proposed to utilize an SNi-like reaction mechanism in which leaving group departure and nucleophilic attack occur on the same face of the hexose. However, significant questions regarding the details of how BshA and similar enzymes accommodate their substrates and facilitate catalysis persist. Here we report X-ray crystallographic structures of BshA from Bacillus subtilis 168 bound with UMP and/or GlcNAc-mal at resolutions of 2.15 and 2.02 Å, respectively. These ligand-bound structures, along with our functional and computational studies, provide clearer insight into how BshA and other retaining GT-B glycosyltransferases operate, corroborating the substrate-assisted, SNi-like reaction mechanism. The analyses presented herein can serve as the basis for the design of inhibitors capable of preventing bacillithiol production and, subsequently, help combat resistance to fosfomycin in various pathogenic Gram-positive microorganisms.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acetyl-alpha-D-glucosaminyl L-malate synthaseA, B379Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: bshAjojHypjHBSU22460
EC: 2.4.1
Find proteins for P42982 (Bacillus subtilis (strain 168))
Explore P42982 
Go to UniProtKB:  P42982
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GMT
Query on GMT

Download CCD File 
A, B
(2S)-2-{[2-acetamido-2-deoxy-alpha-D-glucopyranosyl]oxy}butanedioic acid
C12 H19 N O10
COBMRTSHZAUOCY-BVKYVCSXSA-N
 Ligand Interaction
U5P
Query on U5P

Download CCD File 
B
URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.66α = 90
b = 164.627β = 90
c = 97.729γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
XDSdata scaling
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF32GM093507
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM030910

Revision History 

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.2: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary