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Yorodumi- PDB-8c4i: Ligand-free Crystal Structure of the decameric Sulfofructose Tran... -
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Basic information
| Entry | Database: PDB / ID: 8c4i | |||||||||
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| Title | Ligand-free Crystal Structure of the decameric Sulfofructose Transaldolase BmSF-TAL | |||||||||
Components | BmSF-TAL | |||||||||
Keywords | TRANSFERASE / Transaldolase / Sulfofugar / Decamer | |||||||||
| Function / homology | Function and homology information6-deoxy-6-sulfo-D-fructose transaldolase / transaldolase activity / aldehyde-lyase activity / carbohydrate metabolic process Similarity search - Function | |||||||||
| Biological species | Bacillus aryabhattai (bacteria) | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | |||||||||
Authors | Snow, A.J.D. / Sharma, M. / Davies, G.J. | |||||||||
| Funding support | United Kingdom, 1items
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Citation | Journal: Structure / Year: 2023Title: Structure and mechanism of sulfofructose transaldolase, a key enzyme in sulfoquinovose metabolism. Authors: Alexander J D Snow / Mahima Sharma / Palika Abayakoon / Spencer J Williams / James N Blaza / Gideon J Davies / ![]() 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 ...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. | |||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Download
| PDBx/mmCIF format | 8c4i.cif.gz | 795.6 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb8c4i.ent.gz | 646.6 KB | Display | PDB format |
| PDBx/mmJSON format | 8c4i.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 8c4i_validation.pdf.gz | 495 KB | Display | wwPDB validaton report |
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| Full document | 8c4i_full_validation.pdf.gz | 529.2 KB | Display | |
| Data in XML | 8c4i_validation.xml.gz | 75.6 KB | Display | |
| Data in CIF | 8c4i_validation.cif.gz | 101 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/8c4i ftp://data.pdbj.org/pub/pdb/validation_reports/c4/8c4i | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8bc2C ![]() 8bc3C ![]() 8bc4C C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Assembly
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| Noncrystallographic symmetry (NCS) | NCS domain:
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About Yorodumi



Bacillus aryabhattai (bacteria)
X-RAY DIFFRACTION
United Kingdom, 1items
Citation






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