5WHU

Crystal structure of 3'SL bound ArtB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

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Ligand Structure Quality Assessment 


This is version 2.0 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:  
    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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ArtB protein
A, B, C, D, E, F, G, H, I, J
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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranoseK, N, Q 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G30207PZ
GlyCosmos:  G30207PZ
GlyGen:  G30207PZ
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose
L, M, O, P, R, S
L, M, O, P, R, S
3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G92323ZH
GlyCosmos:  G92323ZH
GlyGen:  G92323ZH
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIA
Query on SIA

Download Ideal Coordinates CCD File 
T [auth A]N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
EA [auth C],
GA [auth D],
NB [auth J],
TA [auth G],
Z [auth B],
EA [auth C],
GA [auth D],
NB [auth J],
TA [auth G],
Z [auth B],
ZA [auth H]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
HB [auth H],
IA [auth D]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth B],
CB [auth H],
DB [auth H],
EB [auth H],
KA [auth E],
AA [auth B],
CB [auth H],
DB [auth H],
EB [auth H],
KA [auth E],
NA [auth F],
OA [auth F],
PA [auth F],
PB [auth J],
U [auth A],
VA [auth G],
WA [auth G]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
AB [auth H],
BB [auth H],
IB [auth I],
JA [auth E],
MA [auth F],
AB [auth H],
BB [auth H],
IB [auth I],
JA [auth E],
MA [auth F],
OB [auth J],
UA [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth B],
CA [auth B],
DA [auth B],
FA [auth C],
FB [auth H],
BA [auth B],
CA [auth B],
DA [auth B],
FA [auth C],
FB [auth H],
GB [auth H],
HA [auth D],
JB [auth I],
KB [auth I],
LA [auth E],
LB [auth I],
MB [auth I],
QA [auth F],
QB [auth J],
RA [auth F],
RB [auth J],
SA [auth F],
V [auth A],
W [auth A],
X [auth A],
XA [auth G],
Y [auth A],
YA [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900025
Query on PRD_900025
L, M, O, P, R, S3'-sialyl-alpha-lactoseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.915α = 90
b = 94.213β = 102.6
c = 123.964γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

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

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: 2020-06-24
    Changes: Data collection, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary