Crystal structure of SQ binding protein from Agrobacterium tumefaciens in complex with sulfoquinovosyl glycerol (SQGro)

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

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Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria.

Sharma, M.Lingford, J.P.Petricevic, M.Snow, A.J.D.Zhang, Y.Jarva, M.A.Mui, J.W.Scott, N.E.Saunders, E.C.Mao, R.Epa, R.da Silva, B.M.Pires, D.E.V.Ascher, D.B.McConville, M.J.Davies, G.J.Williams, S.J.Goddard-Borger, E.D.

(2022) Proc Natl Acad Sci U S A 119

  • DOI: https://doi.org/10.1073/pnas.2116022119
  • Primary Citation of Related Structures:  
    7BBY, 7BBZ, 7BC0, 7BC1, 7NBZ, 7OFX, 7OFY, 7OH2, 7OLF

  • PubMed Abstract: 

    Catabolism of sulfoquinovose (SQ; 6-deoxy-6-sulfoglucose), the ubiquitous sulfosugar produced by photosynthetic organisms, is an important component of the biogeochemical carbon and sulfur cycles. Here, we describe a pathway for SQ degradation that involves oxidative desulfurization to release sulfite and enable utilization of the entire carbon skeleton of the sugar to support the growth of the plant pathogen Agrobacterium tumefaciens SQ or its glycoside sulfoquinovosyl glycerol are imported into the cell by an ATP-binding cassette transporter system with an associated SQ binding protein. A sulfoquinovosidase hydrolyzes the SQ glycoside and the liberated SQ is acted on by a flavin mononucleotide-dependent sulfoquinovose monooxygenase, in concert with an NADH-dependent flavin reductase, to release sulfite and 6-oxo-glucose. An NAD(P)H-dependent oxidoreductase reduces the 6-oxo-glucose to glucose, enabling entry into primary metabolic pathways. Structural and biochemical studies provide detailed insights into the recognition of key metabolites by proteins in this pathway. Bioinformatic analyses reveal that the sulfoquinovose monooxygenase pathway is distributed across Alpha- and Betaproteobacteria and is especially prevalent within the Rhizobiales order. This strategy for SQ catabolism is distinct from previously described pathways because it enables the complete utilization of all carbons within SQ by a single organism with concomitant production of inorganic sulfite.

  • Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington YO10 5DD, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sulfoquinovosyl binding protein
A, B
396Agrobacterium tumefaciensMutation(s): 0 
Gene Names: SY94_3278
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VCW (Subject of Investigation/LOI)
Query on VCW

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
[(2S,3S,4S,5R,6S)-6-[(2R)-2,3-bis(oxidanyl)propoxy]-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid
C9 H18 O10 S
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.795α = 90
b = 137.802β = 118.71
c = 54.068γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Leverhulme TrustUnited KingdomRPG-2017-190

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-04-20
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description