8WCH

Crystal structure of SAR11_0655 bound to a co-purified ligand, L-pyroglutamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 

Starting Model: in silico
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This is version 1.3 of the entry. See complete history


Literature

The ultra-high affinity transport proteins of ubiquitous marine bacteria.

Clifton, B.E.Alcolombri, U.Uechi, G.I.Jackson, C.J.Laurino, P.

(2024) Nature 634: 721-728

  • DOI: https://doi.org/10.1038/s41586-024-07924-w
  • Primary Citation of Related Structures:  
    8HQQ, 8HQR, 8KD0, 8WCH

  • PubMed Abstract: 

    SAR11 bacteria are the most abundant microorganisms in the surface ocean 1 and have global biogeochemical importance 2-4 . To thrive in their competitive oligotrophic environment, these bacteria rely heavily on solute-binding proteins that facilitate uptake of specific substrates via membrane transporters 5,6 . The functions and properties of these transport proteins are key factors in the assimilation of dissolved organic matter and biogeochemical cycling of nutrients in the ocean, but they have remained largely inaccessible to experimental investigation. Here we performed genome-wide experimental characterization of all solute-binding proteins in a prototypical SAR11 bacterium, revealing specific functions and general trends in their properties that contribute to the success of SAR11 bacteria in oligotrophic environments. We found that the solute-binding proteins of SAR11 bacteria have extremely high binding affinity (dissociation constant >20 pM) and high binding specificity, revealing molecular mechanisms of oligotrophic adaptation. Our functional data have uncovered new carbon sources for SAR11 bacteria and enable accurate biogeographical analysis of SAR11 substrate uptake capabilities throughout the ocean. This study provides a comprehensive view of the substrate uptake capabilities of ubiquitous marine bacteria, providing a necessary foundation for understanding their contribution to assimilation of dissolved organic matter in marine ecosystems.


  • Organizational Affiliation

    Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan. benjamin.clifton@oist.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable Leu/Ile/Val-binding protein
A, B
417Candidatus Pelagibacter ubique HTCC1062Mutation(s): 0 
Gene Names: braC
UniProt
Find proteins for Q4FMW4 (Pelagibacter ubique (strain HTCC1062))
Explore Q4FMW4 
Go to UniProtKB:  Q4FMW4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4FMW4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.204α = 90
b = 122.204β = 90
c = 125.908γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-09-18
    Changes: Database references
  • Version 1.2: 2024-09-25
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Database references, Structure summary