4FZR

Crystal Structure of SsfS6, Streptomyces sp. SF2575 glycosyltransferase

• PDB DOI: https://doi.org/10.2210/pdb4FZR/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces sp. SF2575
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-07-07 Released: 2012-07-25 
• Deposition Author(s): Wang, F., Zhou, M., Singh, S., Bingman, C.A., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.262 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 

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

• PubMed: 23526584 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.23 kDa 
• Atom Count: 2,752 
• Modelled Residue Count: 348 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SsfS6	A	398	Streptomyces sp. SF2575	Mutation(s): 0  Gene Names: ssfS6
UniProt
Find proteins for D6MSX4 (Streptomyces sp. SF2575) Explore D6MSX4  Go to UniProtKB:  D6MSX4

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.262 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 
• Space Group: P 6₁ 2 2
• Diffraction Data: https://doi.org/10.18430/m34fzr

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.605	α = 90
b = 82.605	β = 90
c = 230.516	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-25 
Deposition Author(s): Wang, F., Zhou, M., Singh, S., Bingman, C.A., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Revision History  

• 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