8HQR

Crystal structure of the arginine-/lysine-binding protein SAR11_1210 from 'Candidatus Pelagibacter ubique' HTCC1062 bound to arginine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

Starting Model: experimental
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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. [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter
A, B
281Candidatus Pelagibacter ubique HTCC1062Mutation(s): 0 
Gene Names: occTSAR11_1210
UniProt
Find proteins for Q4FLC2 (Pelagibacter ubique (strain HTCC1062))
Explore Q4FLC2 
Go to UniProtKB:  Q4FLC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4FLC2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.128α = 90
b = 84.689β = 90
c = 106.097γ = 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: 2023-12-27
    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