5WHV

Crystal structure of ArtB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1038/s41564-017-0033-2
  • Primary Citation of Related Structures:  
    5WHT, 5WHU, 5WHV

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ArtB protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
149Salmonella enterica subsp. enterica serovar Typhimurium str. DT104Mutation(s): 0 
Gene Names: ArtBERS157243_04891
UniProt
Find proteins for Q404H3 (Salmonella enterica subsp. enterica serovar Typhimurium str. DT104)
Explore Q404H3 
Go to UniProtKB:  Q404H3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ404H3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
DB [auth J]
L [auth A]
OA [auth G]
Q [auth B]
U [auth C]
DB [auth J],
L [auth A],
OA [auth G],
Q [auth B],
U [auth C],
UA [auth H],
YA [auth I]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth E]
CB [auth J]
FA [auth F]
GA [auth F]
HA [auth F]
AA [auth E],
CB [auth J],
FA [auth F],
GA [auth F],
HA [auth F],
IA [auth F],
JA [auth F],
K [auth A],
MA [auth G],
NA [auth G],
O [auth B],
P [auth B],
RA [auth H],
SA [auth H],
T [auth C],
TA [auth H],
W [auth D],
WA [auth I],
XA [auth I],
Y [auth E],
Z [auth E]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
BB [auth I]
DA [auth E]
EA [auth E]
FB [auth J]
LA [auth F]
BB [auth I],
DA [auth E],
EA [auth E],
FB [auth J],
LA [auth F],
N [auth A],
QA [auth G],
S [auth B],
VA [auth H]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AB [auth I]
BA [auth E]
CA [auth E]
EB [auth J]
KA [auth F]
AB [auth I],
BA [auth E],
CA [auth E],
EB [auth J],
KA [auth F],
M [auth A],
PA [auth G],
R [auth B],
V [auth C],
X [auth D],
ZA [auth I]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.872α = 90
b = 94.231β = 103.62
c = 125.23γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2019-01-09
    Changes: Data collection, Derived calculations
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description