9AT9

Crystal structure of Klebsiella pneumoniae FimH lectin domain bound to D-mannose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Conformational ensembles in Klebsiella pneumoniae FimH impact uropathogenesis.

Lopatto, E.D.B.Pinkner, J.S.Sanick, D.A.Potter, R.F.Liu, L.X.Bazan Villicana, J.Tamadonfar, K.O.Ye, Y.Zimmerman, M.I.Gualberto, N.C.Dodson, K.W.Janetka, J.W.Hunstad, D.A.Hultgren, S.J.

(2024) Proc Natl Acad Sci U S A 121: e2409655121-e2409655121

  • DOI: https://doi.org/10.1073/pnas.2409655121
  • Primary Citation of Related Structures:  
    9AT9

  • PubMed Abstract: 

    Klebsiella pneumoniae is an important pathogen causing difficult-to-treat urinary tract infections (UTIs). Over 1.5 million women per year suffer from recurrent UTI, reducing quality of life and causing substantial morbidity and mortality, especially in the hospital setting. Uropathogenic E. coli (UPEC) is the most prevalent cause of UTI. Like UPEC, K. pneumoniae relies on type 1 pili, tipped with the mannose-binding adhesin FimH, to cause cystitis. However, K. pneumoniae FimH is a poor binder of mannose, despite a mannose-binding pocket identical to UPEC FimH. FimH is composed of two domains that are in an equilibrium between tense (low-affinity) and relaxed (high-affinity) conformations. Substantial interdomain interactions in the tense conformation yield a low-affinity, deformed mannose-binding pocket, while domain-domain interactions are broken in the relaxed state, resulting in a high-affinity binding pocket. Using crystallography, we identified the structural basis by which domain-domain interactions direct the conformational equilibrium of K. pneumoniae FimH, which is strongly shifted toward the low-affinity tense state. Removal of the pilin domain restores mannose binding to the lectin domain, thus showing that poor mannose binding by K. pneumoniae FimH is not an inherent feature of the mannose-binding pocket. Phylogenetic analyses of K. pneumoniae genomes found that FimH sequences are highly conserved. However, we surveyed a collection of K. pneumoniae isolates from patients with long-term indwelling catheters and identified isolates that possessed relaxed higher-binding FimH variants, which increased K. pneumoniae fitness in bladder infection models, suggesting that long-term residence within the urinary tract may select for higher-binding FimH variants.


  • Organizational Affiliation

    Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FimHA [auth B]166Klebsiella pneumoniaeMutation(s): 0 
Gene Names: fimHfimH_1fimH_2
UniProt
Find proteins for B0LF88 (Klebsiella pneumoniae)
Explore B0LF88 
Go to UniProtKB:  B0LF88
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0LF88
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MAN (Subject of Investigation/LOI)
Query on MAN

Download Ideal Coordinates CCD File 
B
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.539α = 90
b = 40.626β = 90
c = 101.043γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI029549
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR37 AI048689
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19 AI157797

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release
  • Version 1.1: 2024-10-02
    Changes: Database references