4G2T

Crystal Structure of Streptomyces sp. SF2575 glycosyltransferase SsfS6, complexed with thymidine diphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.7 of the entry. See complete history


Literature

Crystal structure of SsfS6, the putative C-glycosyltransferase involved in SF2575 biosynthesis.

Wang, F.Zhou, M.Singh, S.Yennamalli, R.M.Bingman, C.A.Thorson, J.S.Phillips, G.N.

(2013) Proteins 81: 1277-1282

  • DOI: https://doi.org/10.1002/prot.24289
  • Primary Citation of Related Structures:  
    4FZR, 4G2T

  • PubMed Abstract: 

    The molecule known as SF2575 from Streptomyces sp. is a tetracycline polyketide natural product that displays antitumor activity against murine leukemia P388 in vivo. In the SF2575 biosynthetic pathway, SsfS6 has been implicated as the crucial C-glycosyltransferase (C-GT) that forms the C-C glycosidic bond between the sugar and the SF2575 tetracycline-like scaffold. Here, we report the crystal structure of SsfS6 in the free form and in complex with TDP, both at 2.4 Å resolution. The structures reveal SsfS6 to adopt a GT-B fold wherein the TDP and docked putative aglycon are consistent with the overall C-glycosylation reaction. As one of only a few existing structures for C-glycosyltransferases, the structures described herein may serve as a guide to better understand and engineer C-glycosylation.


  • Organizational Affiliation

    Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SsfS6397Streptomyces sp. SF2575Mutation(s): 0 
Gene Names: ssfS6
UniProt
Find proteins for D6MSX4 (Streptomyces sp. SF2575)
Explore D6MSX4 
Go to UniProtKB:  D6MSX4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6MSX4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TYD
Query on TYD

Download Ideal Coordinates CCD File 
B [auth A]THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.141α = 90
b = 81.141β = 90
c = 229.906γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2012-10-24
    Changes: Derived calculations
  • Version 1.2: 2013-05-01
    Changes: Database references
  • Version 1.3: 2013-07-03
    Changes: Database references
  • Version 1.4: 2017-11-15
    Changes: Refinement description
  • Version 1.5: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2023-12-06
    Changes: Data collection
  • Version 1.7: 2024-10-09
    Changes: Structure summary