8C5N

Sub-atomic resolution structure of the chitin-binding protein D (CbpD) from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.75 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.154 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Immunization with lytic polysaccharide monooxygenase CbpD induces protective immunity against Pseudomonas aeruginosa pneumonia.

Askarian, F.Tsai, C.M.Cordara, G.Zurich, R.H.Bjanes, E.Golten, O.Vinther Sorensen, H.Kousha, A.Meier, A.Chikwati, E.Bruun, J.A.Ludviksen, J.A.Choudhury, B.Trieu, D.Davis, S.Edvardsen, P.K.T.Mollnes, T.E.Liu, G.Y.Krengel, U.Conrad, D.J.Vaaje-Kolstad, G.Nizet, V.

(2023) Proc Natl Acad Sci U S A 120: e2301538120-e2301538120

  • DOI: https://doi.org/10.1073/pnas.2301538120
  • Primary Citation of Related Structures:  
    8C5N

  • PubMed Abstract: 

    Pseudomonas aeruginosa (PA) CbpD belongs to the lytic polysaccharide monooxygenases (LPMOs), a family of enzymes that cleave chitin or related polysaccharides. Here, we demonstrate a virulence role of CbpD in PA pneumonia linked to impairment of host complement function and opsonophagocytic clearance. Following intratracheal challenge, a PA ΔCbpD mutant was more easily cleared and produced less mortality than the wild-type parent strain. The x-ray crystal structure of the CbpD LPMO domain was solved to subatomic resolution (0.75Å) and its two additional domains modeled by small-angle X-ray scattering and Alphafold2 machine-learning algorithms, allowing structure-based immune epitope mapping. Immunization of naive mice with recombinant CbpD generated high IgG antibody titers that promoted human neutrophil opsonophagocytic killing, neutralized enzymatic activity, and protected against lethal PA pneumonia and sepsis. IgG antibodies generated against full-length CbpD or its noncatalytic M2+CBM73 domains were opsonic and protective, even in previously PA-exposed mice, while antibodies targeting the AA10 domain were not. Preexisting antibodies in PA-colonized cystic fibrosis patients primarily target the CbpD AA10 catalytic domain. Further exploration of LPMO family proteins, present across many clinically important and antibiotic-resistant human pathogens, may yield novel and effective vaccine antigens.


  • Organizational Affiliation

    Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chitin-binding protein CbpD193Pseudomonas aeruginosa PA14Mutation(s): 0 
Gene Names: cpbDPA14_53250
UniProt
Find proteins for Q02I11 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore Q02I11 
Go to UniProtKB:  Q02I11
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02I11
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.75 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.6α = 90
b = 54.56β = 99.246
c = 47.98γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
SHELXLrefinement
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Norwegian Research CouncilNorway326272
Norwegian Research CouncilNorway272201
Norwegian Research CouncilNorway245828

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2023-07-26
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary