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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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

  • 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 respectiv ...

    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.USA 93: 10584


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional tail protein
A
559Salmonella phage P22Mutation(s): 0 
Gene Names: 9
Find proteins for P12528 (Salmonella phage P22)
Go to UniProtKB:  P12528
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PZU
Query on PZU

Download SDF File 
Download CCD File 
A
3,6-dideoxy-alpha-D-ribo-hexopyranose
C6 H12 O4
KYPWIZMAJMNPMJ-MOJAZDJTSA-N
 Ligand Interaction
RAM
Query on RAM

Download SDF File 
Download CCD File 
A
ALPHA-L-RHAMNOSE
C6 H12 O5
SHZGCJCMOBCMKK-HGVZOGFYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
GLA
Query on GLA

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Download CCD File 
A
ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-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 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 119.943α = 90.00
b = 119.943β = 90.00
c = 119.943γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
REFMACrefinement
MxCuBEdata collection
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2014-08-13
    Type: Database references