9I1M | pdb_00009i1m

Structure of AauA, a sugar-binding protein with its substrate

• PDB DOI: https://doi.org/10.2210/pdb9I1M/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-16 Released: 2025-07-16 
• Deposition Author(s): Josts, I., Cottam, C., Connolly, J.P.R.
• Funding Organization(s): UK Research and Innovation (UKRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.143 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.126 (Depositor) 
• R-Value Observed: 
  0.127 (Depositor) 

Starting Model: in silico

Literature

Convergent evolution of distinct D-ribulose utilisation pathways in attaching and effacing pathogens.

Cottam, C., Bowran, K., White, R.T., Basle, A., Josts, I., Connolly, J.P.R.

(2025) Nat Commun 16: 6976-6976

• PubMed: 40730545 
• DOI: https://doi.org/10.1038/s41467-025-62476-5
• Primary Citation Related Structures: 
  9I1M


• PubMed Abstract: 
  

  Attaching and effacing pathogens overcome colonisation resistance by competing with metabolically similar organisms for limited resources. Enterohaemorrhagic E. coli (EHEC) utilises the pathogenicity island-encoded Accessory ʟ-arabinose Uptake (Aau) transporter to effectively colonise the mouse gut, hypothesised to be achieved via an enhanced capacity to scavenge ʟ-arabinose. Aau is regulated exclusively in response to ʟ-arabinose, but it is unclear how this system specifically benefits EHEC in vivo. Here, we show that Aau displays a > 200-fold higher affinity for the monosaccharide D-ribulose, over ʟ-arabinose. EHEC cannot grow on D-ribulose as a sole carbon source and this sugar does not trigger aau transcription. However, Aau effectively transports D-ribulose into the cell only in the presence of ʟ-arabinose, where it feeds into the pentose phosphate pathway, after phosphorylation by the ʟ-ribulokinase AraB, thus providing EHEC a significant fitness advantage. EHEC has therefore evolved a mechanism of hijacking the canonical ʟ-arabinose utilisation machinery to promote D-ribulose utilisation in vivo. Furthermore, Citrobacter rodentium encodes an analogous system that exclusively transports D-ribulose and metabolises it via a dedicated D-ribulokinase. These unique mechanisms of D-ribulose utilisation suggest that convergent evolution has driven the ability of distinct pathogenic species to exploit this nutrient during invasion of the gut niche.

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Organizational Affiliation: 
• Newcastle University Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, UK.
New Zealand Institute for Public Health and Forensic Science, Health Security, Porirua, New Zealand.
Newcastle University Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 36.24 kDa 
• Atom Count: 2,492 
• Modeled Residue Count: 292 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar-binding protein	A	328	Escherichia coli	Mutation(s): 0  Gene Names: ECs_0374
UniProt
Find proteins for Q8X6A6 (Escherichia coli O157:H7) Explore Q8X6A6  Go to UniProtKB:  Q8X6A6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	B [auth A], D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
A1IZL	C [auth A]	(2~{S},3~{R},4~{R})-2-(hydroxymethyl)oxolane-2,3,4-triol C5 H10 O5 LQXVFWRQNMEDEE-WDCZJNDASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.143 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.126 (Depositor) 
• R-Value Observed: 0.127 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.38	α = 90
b = 66.94	β = 94.45
c = 57.85	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Josts, I., Cottam, C., Connolly, J.P.R.

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Funding Organization	Location	Grant Number
UK Research and Innovation (UKRI)	United Kingdom	--

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release
  
• Version 1.1: 2026-01-28
  Changes: Database references