9HT4 | pdb_00009ht4

Crystal structure of PA0884, the SBP component of a Pseudomonas aeruginosa PAO1 Tripartite ATP-independent Periplasmic (TRAP) transporter, complexed with succinate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.241 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: in silico
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Literature

Itaconate utilisation by the human pathogen Pseudomonas aeruginosa requires uptake via the IctPQM TRAP transporter.

Mehboob, J.Herman, R.Elston, R.C.Afolabi, H.Kinniment-Williams, B.E.van der Woude, M.W.Wilkinson, A.J.Thomas, G.H.

(2025) Biochem J 482

  • DOI: https://doi.org/10.1042/BCJ20253132
  • Primary Citation of Related Structures:  
    9HT3, 9HT4

  • PubMed Abstract: 

    Pseudomonas aeruginosa PA01 is one of the major causes of disease persistence and mortality in patients with lung pathologies, relying on various host metabolites as carbon and energy sources for growth. The ict-ich-ccl operon (pa0878, pa0882 and pa0883) in PAO1 is required for growth on the host molecule itaconate, a C5-dicarboxylate. However, it is not known how itaconate is taken up into P. aeruginosa. Here, we demonstrate that a genetically linked tripartite ATP-independent periplasmic (TRAP) transporter (pa0884-pa0886), which is homologous to the known C4-dicarboxylate-binding TRAP system, is essential for growth on itaconate, but not for the closely related C4-dicarboxylate succinate. Using tryptophan fluorescence spectroscopy, we demonstrate that the substrate-binding protein (SBP), IctP (PA0884), binds itaconate but still retains higher affinity for the related C4-dicarboxylates. The structures of IctP bound to itaconate (1.80 Å) and succinate (1.75 Å) revealed an enclosed ligand-binding pocket with ion pairing interactions with the ligand carboxylates. The C2 methylene group that is the distinguishing feature of itaconate compared with succinate is accommodated by a unique change in the IctP-binding site from a Leu to Val, which distinguishes it from closely related C4-dicarboxylate-binding SBPs. Together, these data suggest that this transporter, which we name IctPQM, has duplicated from a canonical C4-dicarboxylate transporter, and its evolution towards itaconate specificity enables this pathogen to now access a key metabolite for persistence in the host.


  • Organizational Affiliation
    • Department of Biology, University of York, Wentworth Way, York, YO10 5DD, U.K.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable C4-dicarboxylate-binding periplasmic protein
A, B
308Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: PA0884
UniProt
Find proteins for Q9I561 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I561 
Go to UniProtKB:  Q9I561
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I561
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.241 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.957α = 90
b = 118.525β = 90
c = 167.21γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Database references