8S5B

Crystal structure of the sulfoquinovosyl binding protein (SmoF) from A. tumefaciens sulfo-SMO pathway in complex with SQOctyl ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.226 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Capture-and-release of a sulfoquinovose-binding protein on sulfoquinovose-modified agarose.

Arumapperuma, T.Snow, A.J.D.Lee, M.Sharma, M.Zhang, Y.Lingford, J.P.Goddard-Borger, E.D.Davies, G.J.Williams, S.J.

(2024) Org Biomol Chem 22: 3237-3244

  • DOI: https://doi.org/10.1039/d4ob00307a
  • Primary Citation of Related Structures:  
    8S5B

  • PubMed Abstract: 

    The solute-binding protein (SBP) components of periplasmic binding protein-dependent ATP-binding cassette (ABC)-type transporters often possess exquisite selectivity for their cognate ligands. Maltose binding protein (MBP), the best studied of these SBPs, has been extensively used as a fusion partner to enable the affinity purification of recombinant proteins. However, other SBPs and SBP-ligand based affinity systems remain underexplored. The sulfoquinovose-binding protein SmoF, is a substrate-binding protein component of the ABC transporter cassette in Agrobacterium tumefaciens involved in importing sulfoquinovose (SQ) and its derivatives for SQ catabolism. Here, we show that SmoF binds with high affinity to the octyl glycoside of SQ (octyl-SQ), demonstrating remarkable tolerance to extension of the anomeric substituent. The 3D X-ray structure of the SmoF·octyl-SQ complex reveals accommodation of the octyl chain, which projects to the protein surface, providing impetus for the synthesis of a linker-equipped SQ-amine using a thiol-ene reaction as a key step, and its conjugation to cyanogen bromide modified agarose. We demonstrate the successful capture and release of SmoF from SQ-agarose resin using SQ as competitive eluant, and selectivity for release versus other organosulfonates. We show that SmoF can be captured and purified from a cell lysate, demonstrating the utility of SQ-agarose in capturing SQ binding proteins from complex mixtures. The present work provides a pathway for development of 'capture-and-release' affinity resins for the discovery and study of SBPs.


  • Organizational Affiliation

    School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia. sjwill@unimelb.edu.au.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sulfoquinovosyl glycerol-binding protein SmoF396Agrobacterium tumefaciensMutation(s): 0 
Gene Names: smoFAtu3282
UniProt
Find proteins for A9CEY9 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore A9CEY9 
Go to UniProtKB:  A9CEY9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9CEY9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H5E (Subject of Investigation/LOI)
Query on A1H5E

Download Ideal Coordinates CCD File 
B [auth A][(2~{S},3~{S},4~{S},5~{R},6~{S})-6-octoxy-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid
C14 H28 O8 S
MGTVINCFAITWEK-RGDJUOJXSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.777α = 90
b = 65.851β = 90
c = 107.018γ = 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 KingdomBB/W003805/1
Leverhulme TrustUnited KingdomRPG-2017-190

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references