6R5O

The crystal structure the Glycoside Hydrolase BglX inactive mutant D286N from P. aeruginosa in complex with two glucose molecules


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Catalytic Cycle of Glycoside Hydrolase BglX fromPseudomonas aeruginosaand Its Implications for Biofilm Formation.

Mahasenan, K.V.Batuecas, M.T.De Benedetti, S.Kim, C.Rana, N.Lee, M.Hesek, D.Fisher, J.F.Sanz-Aparicio, J.Hermoso, J.A.Mobashery, S.

(2020) ACS Chem Biol 15: 189-196

  • DOI: https://doi.org/10.1021/acschembio.9b00754
  • Primary Citation of Related Structures:  
    6R5I, 6R5N, 6R5O, 6R5P, 6R5R, 6R5T, 6R5U, 6R5V

  • PubMed Abstract: 

    BglX is a heretofore uncharacterized periplasmic glycoside hydrolase (GH) of the human pathogen Pseudomonas aeruginosa . X-ray analysis identifies it as a protein homodimer. The two active sites of the homodimer comprise catalytic residues provided by each monomer. This arrangement is seen in <2% of the hydrolases of known structure. In vitro substrate profiling shows BglX is a catalyst for β-(1→2) and β-(1→3) saccharide hydrolysis. Saccharides with β-(1→4) or β-(1→6) bonds, and the β-(1→4) muropeptides from the cell-wall peptidoglycan, are not substrates. Additional structural insights from X-ray analysis (including structures of a mutant enzyme-derived Michaelis complex, two transition-state mimetics, and two enzyme-product complexes) enabled the comprehensive description of BglX catalysis. The half-chair ( 4 H 3 ) conformation of the transition-state oxocarbenium species, the approach of the hydrolytic water molecule to the oxocarbenium species, and the stepwise release of the two reaction products were also visualized. The substrate pattern for BglX aligns with the [β-(1→2)-Glc] x and [β-(1→3)-Glc] x periplasmic osmoregulated periplasmic glucans, and possibly with the Psl exopolysaccharides, of P. aeruginosa . Both polysaccharides are implicated in biofilm formation. Accordingly, we show that inactivation of the bglX gene of P. aeruginosa PAO1 attenuates biofilm formation.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic beta-glucosidaseA [auth B],
B [auth A]
733Pseudomonas aeruginosa PAO1Mutation(s): 1 
Gene Names: bglXPA1726
EC: 3.2.1.21
UniProt
Find proteins for Q9I311 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I311 
Go to UniProtKB:  Q9I311
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I311
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.505α = 65.64
b = 74.907β = 74.18
c = 82.102γ = 68.9
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM61629

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2022-03-30
    Changes: Author supporting evidence, Database references, Structure summary
  • Version 1.3: 2024-01-24
    Changes: Data collection, Refinement description