8C4I | pdb_00008c4i

Ligand-free Crystal Structure of the decameric Sulfofructose Transaldolase BmSF-TAL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.268 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.234 (DCC) 

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

Literature

Structure and mechanism of sulfofructose transaldolase, a key enzyme in sulfoquinovose metabolism.

Snow, A.J.D.Sharma, M.Abayakoon, P.Williams, S.J.Blaza, J.N.Davies, G.J.

(2023) Structure 31: 244

  • DOI: https://doi.org/10.1016/j.str.2023.01.010
  • Primary Citation Related Structures: 
    8BC2, 8BC3, 8BC4, 8C4I

  • PubMed Abstract: 

    Sulfoquinovose (SQ) is a key component of plant sulfolipids (sulfoquinovosyl diacylglycerols) and a major environmental reservoir of biological sulfur. Breakdown of SQ is achieved by bacteria through the pathways of sulfoglycolysis. The sulfoglycolytic sulfofructose transaldolase (sulfo-SFT) pathway is used by gut-resident firmicutes and soil saprophytes. After isomerization of SQ to sulfofructose (SF), the namesake enzyme catalyzes the transaldol reaction of SF transferring dihydroxyacetone to 3C/4C acceptors to give sulfolactaldehyde and fructose-6-phosphate or sedoheptulose-7-phosphate. We report the 3D cryo-EM structure of SF transaldolase from Bacillus megaterium in apo and ligand bound forms, revealing a decameric structure formed from two pentameric rings of the protomer. We demonstrate a covalent "Schiff base" intermediate formed by reaction of SF with Lys89 within a conserved Asp-Lys-Glu catalytic triad and defined by an Arg-Trp-Arg sulfonate recognition triad. The structural characterization of the signature enzyme of the sulfo-SFT pathway provides key insights into molecular recognition of the sulfonate group of sulfosugars.


  • Organizational Affiliation
    • Department of Chemistry, York Structural Biology Laboratory, York YO10 5DD, UK.

Macromolecule Content 

  • Total Structure Weight: 253.12 kDa 
  • Atom Count: 16,885 
  • Modeled Residue Count: 2,191 
  • Deposited Residue Count: 2,260 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BmSF-TAL226Priestia aryabhattaiMutation(s): 0 
EC: 2.2.1.14
UniProt
Find proteins for A0A7W3N5X5 (Priestia aryabhattai)
Explore A0A7W3N5X5 
Go to UniProtKB:  A0A7W3N5X5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7W3N5X5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.268 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.234 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.891α = 90
b = 120.839β = 93.401
c = 152.643γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Leverhulme TrustUnited KingdomRPG-2017-190

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-03-08
    Changes: Database references
  • Version 1.2: 2023-03-15
    Changes: Database references
  • Version 1.3: 2023-11-15
    Changes: Data collection, Source and taxonomy