8DKY

Crystal structure of the Aquifex aeolicus Wzt Carbohydrate Binding Domain bound to 3-O-methyl-D-mannose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.261 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Molecular basis for polysaccharide recognition and modulated ATP hydrolysis by the O antigen ABC transporter.

Spellmon, N.Muszynski, A.Gorniak, I.Vlach, J.Hahn, D.Azadi, P.Zimmer, J.

(2022) Nat Commun 13: 5226-5226

  • DOI: https://doi.org/10.1038/s41467-022-32597-2
  • Primary Citation of Related Structures:  
    8DKU, 8DKY, 8DL0, 8DN8, 8DNC, 8DNE, 8DOU

  • PubMed Abstract: 

    O antigens are ubiquitous protective extensions of lipopolysaccharides in the extracellular leaflet of the Gram-negative outer membrane. Following biosynthesis in the cytosol, the lipid-linked polysaccharide is transported to the periplasm by the WzmWzt ABC transporter. Often, O antigen secretion requires the chemical modification of its elongating terminus, which the transporter recognizes via a carbohydrate-binding domain (CBD). Here, using components from A. aeolicus, we identify the O antigen structure with methylated mannose or rhamnose as its cap. Crystal and cryo electron microscopy structures reveal how WzmWzt recognizes this cap between its carbohydrate and nucleotide-binding domains in a nucleotide-free state. ATP binding induces drastic conformational changes of its CBD, terminating interactions with the O antigen. ATPase assays and site directed mutagenesis reveal reduced hydrolytic activity upon O antigen binding, likely to facilitate polymer loading into the ABC transporter. Our results elucidate critical steps in the recognition and translocation of polysaccharides by ABC transporters.


  • Organizational Affiliation

    Howard Hughes Medical Institute, University of Virginia School of Medicine, Charlottesville, VA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter
A, B
144Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: abcT4aq_1094
UniProt
Find proteins for O67181 (Aquifex aeolicus (strain VF5))
Explore O67181 
Go to UniProtKB:  O67181
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67181
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.261 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.561α = 90
b = 58.169β = 90
c = 95.316γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description