6AS8

F9 pilus adhesin FmlH lectin domain from E. coli UTI89 co-crystallized with ortho-biphenyl-2'-carboxyl N-acetyl-beta-galactosaminoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.101 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-based discovery of glycomimetic FmlH ligands as inhibitors of bacterial adhesion during urinary tract infection.

Kalas, V.Hibbing, M.E.Maddirala, A.R.Chugani, R.Pinkner, J.S.Mydock-McGrane, L.K.Conover, M.S.Janetka, J.W.Hultgren, S.J.

(2018) Proc.Natl.Acad.Sci.USA 115: E2819-E2828

  • DOI: 10.1073/pnas.1720140115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Treatment of bacterial infections is becoming a serious clinical challenge due to the global dissemination of multidrug antibiotic resistance, necessitating the search for alternative treatments to disarm the virulence mechanisms underlying these inf ...

    Treatment of bacterial infections is becoming a serious clinical challenge due to the global dissemination of multidrug antibiotic resistance, necessitating the search for alternative treatments to disarm the virulence mechanisms underlying these infections. Uropathogenic Escherichia coli (UPEC) employs multiple chaperone-usher pathway pili tipped with adhesins with diverse receptor specificities to colonize various host tissues and habitats. For example, UPEC F9 pili specifically bind galactose or N -acetylgalactosamine epitopes on the kidney and inflamed bladder. Using X-ray structure-guided methods, virtual screening, and multiplex ELISA arrays, we rationally designed aryl galactosides and N -acetylgalactosaminosides that inhibit the F9 pilus adhesin FmlH. The lead compound, 29β-NAc, is a biphenyl N -acetyl-β-galactosaminoside with a K i of ∼90 nM, representing a major advancement in potency relative to the characteristically weak nature of most carbohydrate-lectin interactions. 29β-NAc binds tightly to FmlH by engaging the residues Y46 through edge-to-face π-stacking with its A-phenyl ring, R142 in a salt-bridge interaction with its carboxylate group, and K132 through water-mediated hydrogen bonding with its N-acetyl group. Administration of 29β-NAc in a mouse urinary tract infection (UTI) model significantly reduced bladder and kidney bacterial burdens, and coadministration of 29β-NAc and mannoside 4Z269, which targets the type 1 pilus adhesin FimH, resulted in greater elimination of bacteria from the urinary tract than either compound alone. Moreover, FmlH specifically binds healthy human kidney tissue in a 29β-NAc-inhibitable manner, suggesting a key role for F9 pili in human kidney colonization. Thus, these glycoside antagonists of FmlH represent a rational antivirulence strategy for UPEC-mediated UTI treatment.


    Organizational Affiliation

    Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110.,Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110.,Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110; janetkaj@wustl.edu hultgren@wustl.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fml fimbrial adhesin FmlD
A, B
166Escherichia coli (strain UTI89 / UPEC)Mutation(s): 0 
Gene Names: fmlD
Find proteins for Q1RBS0 (Escherichia coli (strain UTI89 / UPEC))
Go to UniProtKB:  Q1RBS0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTG
Query on BTG

Download SDF File 
Download CCD File 
A, B
2'-{[2-(acetylamino)-2-deoxy-beta-D-galactopyranosyl]oxy}[1,1'-biphenyl]-3-carboxylic acid
ortho-biphenyl-2'-carboxyl N-acetyl-beta-galactosaminoside
C21 H23 N O8
FLXAKMSHXBTMLT-GQUPQBGVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.101 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.957α = 90.00
b = 51.519β = 90.00
c = 117.496γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States108840

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2019-09-11
    Type: Data collection, Database references
  • Version 1.2: 2019-12-25
    Type: Author supporting evidence