2X6W

Tailspike protein mutant E372Q of E.coli bacteriophage HK620 in complex with hexasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.124 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Single Amino Acid Exchange in Bacteriophage Hk620 Tailspike Protein Results in Thousand-Fold Increase of its Oligosaccharide Affinity.

Broeker, N.K.Gohlke, U.Muller, J.J.Uetrecht, C.Heinemann, U.Seckler, R.Barbirz, S.

(2013) Glycobiology 23: 59

  • DOI: 10.1093/glycob/cws126
  • Primary Citation of Related Structures:  
    2X6W, 2X6X, 2X6Y, 2X85, 4AVZ

  • PubMed Abstract: 
  • Bacteriophage HK620 recognizes and cleaves the O-antigen polysaccharide of Escherichia coli serogroup O18A1 with its tailspike protein (TSP). HK620TSP binds hexasaccharide fragments with low affinity, but single amino acid exchanges generated a set of high-affinity mutants with submicromolar dissociation constants ...

    Bacteriophage HK620 recognizes and cleaves the O-antigen polysaccharide of Escherichia coli serogroup O18A1 with its tailspike protein (TSP). HK620TSP binds hexasaccharide fragments with low affinity, but single amino acid exchanges generated a set of high-affinity mutants with submicromolar dissociation constants. Isothermal titration calorimetry showed that only small amounts of heat were released upon complex formation via a large number of direct and solvent-mediated hydrogen bonds between carbohydrate and protein. At room temperature, association was both enthalpy- and entropy-driven emphasizing major solvent rearrangements upon complex formation. Crystal structure analysis showed identical protein and sugar conformers in the TSP complexes regardless of their hexasaccharide affinity. Only in one case, a TSP mutant bound a different hexasaccharide conformer. The extended sugar binding site could be dissected in two regions: first, a hydrophobic pocket at the reducing end with minor affinity contributions. Access to this site could be blocked by a single aspartate to asparagine exchange without major loss in hexasaccharide affinity. Second, a region where the specific exchange of glutamate for glutamine created a site for an additional water molecule. Side-chain rearrangements upon sugar binding led to desolvation and additional hydrogen bonding which define this region of the binding site as the high-affinity scaffold.


    Related Citations: 
    • Crystal Structure of Escherichia Coli Phage Hk620 Tailspike: Podoviral Tailspike Endoglycosidase Modules are Evolutionarily Related.
      Barbirz, S., Muller, J.J., Uetrecht, C., Clark, A.J., Heinemann, U., Seckler, R.
      (2008) Mol Microbiol 69: 303

    Organizational Affiliation

    Physikalische Biochemie, Universität Potsdam, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TAIL SPIKE PROTEINA600Enterobacteria phage HK620Mutation(s): 1 
Gene Names: 9
UniProt
Find proteins for Q9AYY6 (Enterobacteria phage HK620)
Explore Q9AYY6 
Go to UniProtKB:  Q9AYY6
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[alpha-L-rhamnopyranose-(1-6)-alpha-D-glucopyranose-(1-4)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)]alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-glucopyranoseB7N/AN/A Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
F [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.124 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.53α = 90
b = 74.53β = 90
c = 174.61γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-02
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references, Structure summary, Version format compliance
  • Version 1.2: 2017-07-12
    Changes: Derived calculations
  • Version 1.3: 2019-01-30
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 1.4: 2019-02-06
    Changes: Data collection, Experimental preparation
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary