5WHT

Crystal structure of 3'SL bound PltB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.932 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Evolution of host adaptation in the Salmonella typhoid toxin.

Gao, X.Deng, L.Stack, G.Yu, H.Chen, X.Naito-Matsui, Y.Varki, A.Galan, J.E.

(2017) Nat Microbiol 2: 1592-1599

  • DOI: 10.1038/s41564-017-0033-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The evolution of virulence traits is central for the emergence or re-emergence of microbial pathogens and for their adaptation to a specific host <sup>1-5 </sup> . Typhoid toxin is an essential virulence factor of the human-adapted bacterial pathoge ...

    The evolution of virulence traits is central for the emergence or re-emergence of microbial pathogens and for their adaptation to a specific host 1-5 . Typhoid toxin is an essential virulence factor of the human-adapted bacterial pathogen Salmonella Typhi 6,7 , the cause of typhoid fever in humans 8-12 . Typhoid toxin has a unique A 2 B 5 architecture with two covalently linked enzymatic 'A' subunits, PltA and CdtB, associated with a homopentameric 'B' subunit made up of PltB, which has binding specificity for the N-acetylneuraminic acid (Neu5Ac) sialoglycans 6,13 prominently present in humans 14 . Here, we examine the functional and structural relationship between typhoid toxin and ArtAB, an evolutionarily related AB 5 toxin encoded by the broad-host Salmonella Typhimurium 15 . We find that ArtA and ArtB, homologues of PltA and PltB, can form a functional complex with the typhoid toxin CdtB subunit after substitution of a single amino acid in ArtA, while ArtB can form a functional complex with wild-type PltA and CdtB. We also found that, after addition of a single-terminal Cys residue, a CdtB homologue from cytolethal distending toxin can form a functional complex with ArtA and ArtB. In line with the broad host specificity of S. Typhimurium, we found that ArtB binds human glycans, terminated in N-acetylneuraminic acid, as well as glycans terminated in N-glycolylneuraminic acid (Neu5Gc), which are expressed in most other mammals 14 . The atomic structure of ArtB bound to its receptor shows the presence of an additional glycan-binding site, which broadens its binding specificity. Despite equivalent toxicity in vitro, we found that the ArtB/PltA/CdtB chimaeric toxin exhibits reduced lethality in an animal model, indicating that the host specialization of typhoid toxin has optimized its targeting mechanisms to the human host. This is a remarkable example of a toxin evolving to broaden its enzymatic activities and adapt to a specific host.


    Organizational Affiliation

    Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06536, USA. jorge.galan@yale.edu.,GlycoMimetics, Inc., 9708 Medical Center Drive, Rockville, MD, 20850, USA.,Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06536, USA.,Glycobiology Research and Training Center, Departments of Medicine, Pathology and Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Chemistry, University of California Davis, Davis, CA, 95616, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative pertussis-like toxin subunit
A, B, C, D, E
138Salmonella typhiMutation(s): 0 
Find proteins for Q8Z6A3 (Salmonella typhi)
Go to UniProtKB:  Q8Z6A3
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C, D, E
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A, C
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
B, D, E
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SIA
Query on SIA

Download SDF File 
Download CCD File 
A, B, C, D
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.932 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.379α = 90.00
b = 95.682β = 90.00
c = 117.173γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-07-18 
  • Released Date: 2017-10-25 
  • Deposition Author(s): Gao, X., Galan, J.E.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI079022

Revision History 

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references
  • Version 1.2: 2019-12-11
    Type: Author supporting evidence, Data collection