5JS4

Crystal structure of phiAB6 tailspike


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 

wwPDB Validation 3D Report Full Report



Literature

Structural basis for fragmenting the exopolysaccharide of Acinetobacter baumannii by bacteriophage Phi AB6 tailspike protein

Lee, I.M.Tu, I.F.Yang, F.L.Ko, T.P.Liao, J.H.Lin, N.T.Wu, C.Y.Ren, C.T.Wang, A.H.Chang, C.M.Huang, K.F.Wu, S.H.

(2017) Sci Rep 7: 42711-42711

  • DOI: 10.1038/srep42711
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • With an increase in antibiotic-resistant strains, the nosocomial pathogen Acinetobacter baumannii has become a serious threat to global health. Glycoconjugate vaccines containing fragments of bacterial exopolysaccharide (EPS) are an emerging therapeu ...

    With an increase in antibiotic-resistant strains, the nosocomial pathogen Acinetobacter baumannii has become a serious threat to global health. Glycoconjugate vaccines containing fragments of bacterial exopolysaccharide (EPS) are an emerging therapeutic to combat bacterial infection. Herein, we characterize the bacteriophage ΦAB6 tailspike protein (TSP), which specifically hydrolyzed the EPS of A. baumannii strain 54149 (Ab-54149). Ab-54149 EPS exhibited the same chemical structure as two antibiotic-resistant A. baumannii strains. The ΦAB6 TSP-digested products comprised oligosaccharides of two repeat units, typically with stoichiometric pseudaminic acid (Pse). The 1.48-1.89-Å resolution crystal structures of an N-terminally-truncated ΦAB6 TSP and its complexes with the semi-hydrolyzed products revealed a trimeric β-helix architecture that bears intersubunit carbohydrate-binding grooves, with some features unusual to the TSP family. The structures suggest that Pse in the substrate is an important recognition site for ΦAB6 TSP. A region in the carbohydrate-binding groove is identified as the determinant of product specificity. The structures also elucidated a retaining mechanism, for which the catalytic residues were verified by site-directed mutagenesis. Our findings provide a structural basis for engineering the enzyme to produce desired oligosaccharides, which is useful for the development of glycoconjugate vaccines against A. baumannii infection.


    Organizational Affiliation

    Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
phiAB6 tailspike
A, B, C
719Bacteriophage sp.Mutation(s): 0 
Find proteins for A0A159BDB5 (Acinetobacter phage phiAB6)
Go to UniProtKB:  A0A159BDB5
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLA
Query on MLA

Download CCD File 
A, B, C
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.018α = 90
b = 77.98β = 100.46
c = 248.08γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Sciences and Technology and Academia SinicaTaiwanNSC101-2923-B-001-005-MY3, MOST104-2325-B-001-003, NSC-101-2319-B-001-003, and MOST105-0210-01-12-01

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release