7EE6

Crystal structure of PltC toxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular Insights into the Assembly and Functional Diversification of Typhoid Toxin.

Liu, X.Chen, Z.Jiao, X.Jiang, X.Qiu, J.You, F.Long, H.Cao, H.Fowler, C.C.Gao, X.

(2022) mBio 13

  • DOI: https://doi.org/10.1128/mbio.01916-21
  • Primary Citation of Related Structures:  
    7EE3, 7EE4, 7EE5, 7EE6

  • PubMed Abstract: 

    Typhoid toxin is an A 2 B 5 protein toxin and an important virulence factor for the human-adapted bacterial pathogen Salmonella enterica serovar Typhi, the causative agent of typhoid fever. Typhoid toxin contains two enzymatic subunits, PltA and CdtB, which dock onto a pentameric delivery platform composed of the protein PltB. It was recently reported that the same enzymatic subunits can assemble with a different delivery platform composed of the protein PltC, forming a distinct version of typhoid toxin. However, the differences in structure and receptor specificity between the PltC and PltB typhoid toxins remain unknown. Here, we determined atomic-level structures of the pentameric PltC subunit, the fully assembled PltC typhoid toxin, and the PltC pentamers in complex with glycan receptors. Biochemical and structural analyses indicate that PltB and PltC are unable to form heteromeric delivery complexes due to electrostatic repulsion at the subunit interface and thus form separate toxins only. We further observed that, despite low sequence similarity between PltB and PltC, they interact with PltA in a similar manner but that PltC exhibits stronger electrostatic interactions with PltA, enabling it to outcompete PltB in toxin assembly. The ligand-bound atomic structures of PltC show an additional glycan binding site not found in PltB and glycan array analysis indicates that PltB and PltC exhibit significant differences in glycan binding specificity. Collectively, this study offers atomic-level insights into how S . Typhi produces two distinct versions of typhoid toxin, thereby generating functional diversity in this key virulence factor. IMPORTANCE Typhoid fever is a devastating disease that kills more than 115,000 people every year and is caused by Salmonella Typhi. Typhoid toxin, exclusively produced by S . Typhi, was demonstrated to be responsible for the pathogenesis of typhoid fever. Typhoid toxin consists of a pentameric delivery B subunit to transport the catalytic A subunits into the host cell through binding of the glycan receptors. Recent study shows that S . Typhi encodes two homologous delivery B subunits that are able to associate with the same active subunits to produce alternative toxins with distinct functional characteristics. Here, we show that the two delivery subunits can form only homopentameric delivery platforms that compete to associate with typhoid toxin's active subunits and that the two resulting toxins have distinct glycan-binding properties that confer distinct functional traits. These findings highlight the unique assembly and functional diversification of typhoid toxins.


  • Organizational Affiliation

    State Key Laboratory of Microbial Technology, Shandong Universitygrid.27255.37, Qingdao, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Subtilase cytotoxin subunit B-like protein
A, B, C, D, E
120Salmonella enterica subsp. enterica serovar Typhi str. CT18Mutation(s): 0 
UniProt
Find proteins for A0A716TY65 (Salmonella enterica subsp. enterica serovar Typhi str. CT18)
Explore A0A716TY65 
Go to UniProtKB:  A0A716TY65
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A716TY65
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytolethal distending toxin subunit B family protein248Salmonella enterica subsp. enterica serovar Typhi str. CT18Mutation(s): 0 
UniProt
Find proteins for A0A718C6E5 (Salmonella enterica subsp. enterica serovar Typhi str. CT18)
Explore A0A718C6E5 
Go to UniProtKB:  A0A718C6E5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A718C6E5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Pertussis-like toxin subunit ArtA224Salmonella enterica subsp. enterica serovar Typhi str. CT18Mutation(s): 0 
UniProt
Find proteins for A0A716AET8 (Salmonella enterica subsp. enterica serovar Typhi str. CT18)
Explore A0A716AET8 
Go to UniProtKB:  A0A716AET8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A716AET8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download Ideal Coordinates CCD File 
FA [auth F],
JA [auth G]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
GA [auth F]
H [auth A]
KA [auth G]
AA [auth E],
BA [auth E],
GA [auth F],
H [auth A],
KA [auth G],
L [auth B],
LA [auth G],
V [auth D],
W [auth D],
X [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
DA [auth E]
EA [auth E]
HA [auth F]
IA [auth F]
K [auth A]
DA [auth E],
EA [auth E],
HA [auth F],
IA [auth F],
K [auth A],
Q [auth B],
R [auth B],
T [auth C],
U [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACN
Query on ACN

Download Ideal Coordinates CCD File 
CA [auth E]
I [auth A]
J [auth A]
M [auth B]
MA [auth G]
CA [auth E],
I [auth A],
J [auth A],
M [auth B],
MA [auth G],
N [auth B],
NA [auth G],
O [auth B],
OA [auth G],
P [auth B],
PA [auth G],
QA [auth G],
RA [auth G],
S [auth C],
Y [auth D],
Z [auth D]
ACETONE
C3 H6 O
CSCPPACGZOOCGX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.997α = 90
b = 184.17β = 90
c = 68.838γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770143

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2022-12-07
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description