8F73

Crystal structure of Pseudomonas aeruginosa UDP-glucose phosphorylase in complex with UDP-glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Tetramerization is essential for the enzymatic function of the Pseudomonas aeruginosa virulence factor UDP-glucose pyrophosphorylase.

Dirr, L.Cleeves, S.Ramon Roth, I.Li, L.Fiebig, T.Ve, T.Haussler, S.Braun, A.von Itzstein, M.Fuhring, J.I.

(2024) mBio 15: e0211423-e0211423

  • DOI: https://doi.org/10.1128/mbio.02114-23
  • Primary Citation of Related Structures:  
    8F73

  • PubMed Abstract: 

    Multidrug-resistant bacteria such as the opportunistic pathogen Pseudomonas aeruginosa , which causes life-threatening infections especially in immunocompromised individuals and cystic fibrosis patients, pose an increasing threat to public health. In the search for new treatment options, P. aeruginosa uridine diphosphate-glucose pyrophosphorylase (PaUGP) has been proposed as a novel drug target because it is required for the biosynthesis of important virulence factors and linked to pathogenicity in animal models. Here, we show that UGP-deficient P. aeruginosa exhibits severely reduced virulence against human lung tissue and cells, emphasizing the enzyme's suitability as a drug target. To establish a basis for the development of selective PaUGP inhibitors, we solved the product-bound crystal structure of tetrameric PaUGP and conducted a comprehensive structure-function analysis, identifying key residues at two different molecular interfaces that are essential for tetramer integrity and catalytic activity and demonstrating that tetramerization is pivotal for PaUGP function. Importantly, we show that part of the PaUGP oligomerization interface is uniquely conserved across bacterial UGPs but does not exist in the human enzyme, therefore representing an allosteric site that may be targeted to selectively inhibit bacterial UGPs.IMPORTANCEInfections with the opportunistic bacterial pathogen Pseudomonas aeruginosa are becoming increasingly difficult to treat due to multidrug resistance. Here, we show that the enzyme uridine diphosphate-glucose pyrophosphorylase (UGP) is involved in P. aeruginosa virulence toward human lung tissue and cells, making it a potential target for the development of new antibacterial drugs. Our exploration of P. aeruginosa (Pa)UGP structure-function relationships reveals that the activity of PaUGP depends on the formation of a tetrameric enzyme complex. We found that a molecular interface involved in tetramer formation is conserved in all bacterial UGPs but not in the human enzyme, and therefore hypothesize that it provides an ideal point of attack to selectively inhibit bacterial UGPs and exploit them as drug targets.


  • Organizational Affiliation

    Institute for Glycomics, Gold Coast Campus, Griffith University, Gold Coast, Queensland, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UTP--glucose-1-phosphate uridylyltransferase
A, B, C, D, E
A, B, C, D, E, F, G, H
285Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: galUPA2023
EC: 2.7.7.9
UniProt
Find proteins for Q9I291 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I291 
Go to UniProtKB:  Q9I291
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I291
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UPG (Subject of Investigation/LOI)
Query on UPG

Download Ideal Coordinates CCD File 
AA [auth H]
I [auth A]
L [auth B]
O [auth C]
R [auth D]
AA [auth H],
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
W [auth F],
Y [auth G]
URIDINE-5'-DIPHOSPHATE-GLUCOSE
C15 H24 N2 O17 P2
HSCJRCZFDFQWRP-JZMIEXBBSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth A],
P [auth C],
S [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
N [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth H]
K [auth A]
M [auth B]
Q [auth C]
T [auth D]
BA [auth H],
K [auth A],
M [auth B],
Q [auth C],
T [auth D],
V [auth E],
X [auth F],
Z [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.715α = 90
b = 114.847β = 97.39
c = 155.761γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
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 Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1157150

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Database references