8C5N | pdb_00008c5n

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

• PDB DOI: https://doi.org/10.2210/pdb8C5N/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas aeruginosa PA14
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-01-09 Released: 2023-06-28 
• Deposition Author(s): Cordara, G., Krengel, U., Golten, O., Vaaje-Kolstad, G., Vinther Soerensen, H.
• Funding Organization(s): Norwegian Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.75 Å
• R-Value Free: 
  0.163 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.151 (DCC) 

Starting Model: experimental

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

• PubMed: 37459522 
• DOI: https://doi.org/10.1073/pnas.2301538120
• Primary Citation 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.

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Organizational Affiliation: 
• Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093.
Department of Chemistry, University of Oslo, N-0315 Oslo, Norway.
Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway.
Division of Critical Care, Department of Anesthesiology, University of California San Diego, La Jolla, CA 92037.
Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, N-1432 Ås, Norway.
Proteomics and Metabolomics Core Facility, Department of Medical Biology, The Arctic University of Norway, N-9037 Tromsø, Norway.
Research Laboratory, Nordland Hospital, N-8005 Bodø, Norway.
Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093.
School of Pharmacy, University of California San Francisco, San Francisco, CA 94143.
Department of Immunology, University of Oslo Hospital, N-0424 Oslo, Norway.
Center of Molecular Inflammation Research, Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, La Jolla, CA 92037.
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 20.97 kDa 
• Atom Count: 1,768 
• Modeled Residue Count: 186 
• Deposited Residue Count: 193 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitin-binding protein CbpD	A	193	Pseudomonas aeruginosa PA14	Mutation(s): 0  Gene Names: cpbD, PA14_53250
UniProt
Find proteins for Q02I11 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Explore Q02I11  Go to UniProtKB:  Q02I11

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	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 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.151 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.6	α = 90
b = 54.56	β = 99.246
c = 47.98	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
SHELXL	refinement
PHENIX	refinement
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-28 
Deposition Author(s): Cordara, G., Krengel, U., Golten, O., Vaaje-Kolstad, G., Vinther Soerensen, H.

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Funding Organization	Location	Grant Number
Norwegian Research Council	Norway	326272
Norwegian Research Council	Norway	272201
Norwegian Research Council	Norway	245828

Revision History  

• 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