7OFX

Crystal structure of a GH31 family sulfoquinovosidase mutant D455N from Agrobacterium tumefaciens in complex with sulfoquinovosyl glycerol (SQGro)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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; gideon.davies@york.ac.uk sjwill@unimelb.edu.au goddard-borger.e@wehi.edu.au.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-glucosidase yihQA,
B [auth C],
C [auth D],
D [auth B]
672Agrobacterium tumefaciensMutation(s): 3 
Gene Names: SY94_3281
EC: 3.2.1.20
UniProt
Find proteins for A9CEZ0 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore A9CEZ0 
Go to UniProtKB:  A9CEZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9CEZ0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.534α = 90
b = 168.396β = 116.53
c = 100.687γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
MOLREPphasing

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