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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  
  • Also Cited By: 4XQI, 4XQH, 6G0X, 4XM3, 4YEL, 4YEJ, 4XR6, 4XQF, 4XOT, 4XOR, 4XOP, 4XON, 4XNF, 4XN3, 4XN0, 4XMY, 4XLH, 4XLF, 4XLE, 4XLC, 4XLA, 4XL9, 4XKW, 4XKV

  • 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 o ...

    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, Universit├Ąt Potsdam, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TAIL SPIKE PROTEIN
A
600Salmonella phage HK620Mutation(s): 1 
Gene Names: 9
Find proteins for Q9AYY6 (Salmonella phage HK620)
Go to UniProtKB:  Q9AYY6
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
RAM
Query on RAM

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

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Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
NDG
Query on NDG

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Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-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
TRS
Query on TRS

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Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 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 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.530α = 90.00
b = 74.530β = 90.00
c = 174.610γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-02
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Database references, Structure summary, Version format compliance
  • Version 1.2: 2017-07-12
    Type: Derived calculations