9G17 | pdb_00009g17

Structure of PslG with a covalently- bound pentasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.174 (Depositor), 0.172 (DCC) 
  • R-Value Work: 
    0.142 (Depositor), 0.139 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Bespoke Activity-Based Probes Reveal that the Pseudomonas aeruginosa Endoglycosidase, PslG, Is an Endo-beta-glucanase.

Ruijgrok, G.Offen, W.A.Pickles, I.B.Raju, D.Patsos, T.de Boer, C.Ofman, T.Rompa, J.van Oord, D.Dodson, E.J.Beekers, A.Voskuilen, T.Ferrari, M.Wu, L.Janssen, A.P.A.Codee, J.D.C.Howell, P.L.Davies, G.J.Overkleeft, H.S.

(2025) J Am Chem Soc 147: 8578-8586

  • DOI: https://doi.org/10.1021/jacs.4c16806
  • Primary Citation of Related Structures:  
    9G17, 9G18

  • PubMed Abstract: 

    During infection, the human opportunistic pathogen Pseudomonas aeruginosa forms protective biofilms, whose matrix consists of proteins, nucleic acids, and polysaccharides such as alginate, Psl, and Pel. Psl, a polymeric pentasaccharide composed of mannose, rhamnose, and glucose, is produced during the early stages of biofilm formation, serving as a protective barrier against antibiotics and the immune system. The Psl biosynthesis gene cluster, besides encoding various glycosyltransferases, also includes an endoglycosidase, PslG. Here, we show, by activity-based protein profiling, structural studies on enzyme-inhibitor complexes, and defined substrate processing, that PslG is not, as previously suggested, an endo-β-mannosidase but instead a retaining endo-β-glucosidase. This insight allows the design of both competitive and covalent PslG inhibitors, as we show for repeating pentasaccharide mimetics featuring either a reducing end deoxynojirimycin or cyclophellitol moiety. This work provides valuable tools to deepen the understanding of Psl biosynthesis, its function in biofilm formation, and its contribution to antibiotic resistance. We demonstrate the enzyme's actual endo-β-glucosidase activity, a means to monitor PslG activity in P. aeruginosa biofilms, and a blueprint for inhibitor design.


  • Organizational Affiliation
    • Leiden Institute of Chemistry, Leiden University, 2300 RA Leiden, The Netherlands.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PslG416Pseudomonas aeruginosaMutation(s): 0 
Gene Names: pslGPA2237
UniProt
Find proteins for Q9I1N2 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I1N2 
Go to UniProtKB:  Q9I1N2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I1N2
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-alpha-L-rhamnopyranose-(1-3)-(1R,2S,4S,5R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol
B
5N/AN/A
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.174 (Depositor), 0.172 (DCC) 
  • R-Value Work:  0.142 (Depositor), 0.139 (DCC) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.692α = 90
b = 97.692β = 90
c = 119.775γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union951231

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Database references