4FZR

Crystal Structure of SsfS6, Streptomyces sp. SF2575 glycosyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.397 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1002/prot.24289
  • Primary Citation of Related Structures:  

  • 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-glyc ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SsfS6
A
398Streptomyces sp. SF2575Mutation(s): 0 
Gene Names: ssfS6
Find proteins for D6MSX4 (Streptomyces sp. SF2575)
Go to UniProtKB:  D6MSX4
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 82.605α = 90.00
b = 82.605β = 90.00
c = 230.516γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-2000data scaling
DENZOdata reduction
HKL-2000data collection
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2012-10-24
    Type: Derived calculations
  • Version 1.2: 2013-05-01
    Type: Database references
  • Version 1.3: 2013-07-03
    Type: Database references
  • Version 1.4: 2017-11-15
    Type: Refinement description