Structure of the sialic acid bound Tripartite ATP-independent Periplasmic (TRAP) periplasmic component SiaP from Photobacterium profundum

Experimental Data Snapshot

  • Resolution: 1.04 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.124 

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This is version 1.2 of the entry. See complete history


Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter.

Davies, J.S.Currie, M.J.North, R.A.Scalise, M.Wright, J.D.Copping, J.M.Remus, D.M.Gulati, A.Morado, D.R.Jamieson, S.A.Newton-Vesty, M.C.Abeysekera, G.S.Ramaswamy, S.Friemann, R.Wakatsuki, S.Allison, J.R.Indiveri, C.Drew, D.Mace, P.D.Dobson, R.C.J.

(2023) Nat Commun 14: 1120-1120

  • DOI: https://doi.org/10.1038/s41467-023-36590-1
  • Primary Citation of Related Structures:  
    7QHA, 7T3E, 8B01

  • PubMed Abstract: 

    In bacteria and archaea, tripartite ATP-independent periplasmic (TRAP) transporters uptake essential nutrients. TRAP transporters receive their substrates via a secreted soluble substrate-binding protein. How a sodium ion-driven secondary active transporter is strictly coupled to a substrate-binding protein is poorly understood. Here we report the cryo-EM structure of the sialic acid TRAP transporter SiaQM from Photobacterium profundum at 2.97 Å resolution. SiaM comprises a "transport" domain and a "scaffold" domain, with the transport domain consisting of helical hairpins as seen in the sodium ion-coupled elevator transporter VcINDY. The SiaQ protein forms intimate contacts with SiaM to extend the size of the scaffold domain, suggesting that TRAP transporters may operate as monomers, rather than the typically observed oligomers for elevator-type transporters. We identify the Na + and sialic acid binding sites in SiaM and demonstrate a strict dependence on the substrate-binding protein SiaP for uptake. We report the SiaP crystal structure that, together with docking studies, suggest the molecular basis for how sialic acid is delivered to the SiaQM transporter complex. We thus propose a model for substrate transport by TRAP proteins, which we describe herein as an 'elevator-with-an-operator' mechanism.

  • Organizational Affiliation

    Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRAP-type C4-dicarboxylate transport system, periplasmic component
A, B
300Photobacterium profundumMutation(s): 0 
Gene Names: SMB20295PBPRA2281
Membrane Entity: Yes 
Find proteins for Q6LPV9 (Photobacterium profundum (strain SS9))
Explore Q6LPV9 
Go to UniProtKB:  Q6LPV9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6LPV9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.04 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.124 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.596α = 90
b = 87.313β = 90
c = 129.412γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Marsden FundNew ZealandUOC1506
Ministry of Business, Innovation and Employment (New Zealand)New ZealandUOCX1706

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references, Structure summary
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description