3TH0

P22 Tailspike complexed with S.Paratyphi O antigen octasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

An essential serotype recognition pocket on phage P22 tailspike protein forces Salmonella enterica serovar Paratyphi A O-antigen fragments to bind as nonsolution conformers.

Andres, D.Gohlke, U.Broeker, N.K.Schulze, S.Rabsch, W.Heinemann, U.Barbirz, S.Seckler, R.

(2013) Glycobiology 23: 486-494

  • DOI: 10.1093/glycob/cws224
  • Primary Citation of Related Structures:  
    3TH0

  • PubMed Abstract: 
  • Bacteriophage P22 recognizes O-antigen polysaccharides of Salmonella enterica subsp. enterica (S.) with its tailspike protein (TSP). In the serovars S. Typhimurium, S. Enteritidis, and S. Paratyphi A, the tetrasaccharide repeat units of the respective O-antigens consist of an identical main chain trisaccharide but different 3,6-dideoxyhexose substituents ...

    Bacteriophage P22 recognizes O-antigen polysaccharides of Salmonella enterica subsp. enterica (S.) with its tailspike protein (TSP). In the serovars S. Typhimurium, S. Enteritidis, and S. Paratyphi A, the tetrasaccharide repeat units of the respective O-antigens consist of an identical main chain trisaccharide but different 3,6-dideoxyhexose substituents. Here, the epimers abequose, tyvelose and paratose determine the specific serotype. P22 TSP recognizes O-antigen octasaccharides in an extended binding site with a single 3,6-dideoxyhexose binding pocket. We have isolated S. Paratyphi A octasaccharides which were not available previously and determined the crystal structure of their complex with P22 TSP. We discuss our data together with crystal structures of complexes with S. Typhimurium and S. Enteritidis octasaccharides determined earlier. Isothermal titration calorimetry showed that S. Paratyphi A octasaccharide binds P22 TSP less tightly, with a difference in binding free energy of ∼7 kJ mol(-1) at 20°C compared with S. Typhimurium and S. Enteritidis octasaccharides. Individual protein-carbohydrate contacts were probed by amino acid replacements showing that the dideoxyhexose pocket contributes to binding of all three serotypes. However, S. Paratyphi A octasaccharides bind in a conformation with an energetically unfavorable ϕ/ψ glycosidic bond angle combination. In contrast, octasaccharides from the other serotypes bind as solution-like conformers. Two water molecules are conserved in all P22 TSP complexes with octasaccharides of different serotypes. They line the dideoxyhexose binding pocket and force the S. Paratyphi A octasaccharides to bind as nonsolution conformers. This emphasizes the role of solvent as part of carbohydrate binding sites.


    Related Citations: 
    • Crystal structure of P22 tailspike protein: interdigitated subunits in a thermostable trimer.
      Steinbacher, S., Seckler, R., Miller, S., Steipe, B., Huber, R., Reinemer, P.
      (1994) Science 265: 383
    • Crystal structure of phage P22 tailspike protein complexed with Salmonella sp. O-antigen receptors.
      Steinbacher, S., Baxa, U., Miller, S., Weintraub, A., Seckler, R., Huber, R.
      (1996) Proc Natl Acad Sci U S A 93: 10584

    Organizational Affiliation

    Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional tail proteinA559Salmonella virus P22Mutation(s): 0 
Gene Names: 9phage p22 gene 9
EC: 3.2.1
UniProt
Find proteins for P12528 (Salmonella phage P22)
Explore P12528 
Go to UniProtKB:  P12528
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-galactopyranose-(1-2)-[alpha-D-Paratopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-alpha-L-rhamnopyranose-(1-3)-alpha-D-galactopyranose-(1-2)-[alpha-D-Paratopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-alpha-L-rhamnopyranoseB8N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G37824OY
GlyCosmos:  G37824OY
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.943α = 90
b = 119.943β = 90
c = 119.943γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary