3UYL

Spinosyn Rhamnosyltransferase SpnG complexed with thymidine diphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Studies of the Spinosyn Rhamnosyltransferase, SpnG.

Isiorho, E.A.Liu, H.W.Keatinge-Clay, A.T.

(2012) Biochemistry 51: 1213-1222

  • DOI: 10.1021/bi201860q
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Spinosyns A and D (spinosad), like many other complex polyketides, are tailored near the end of their biosyntheses through the addition of sugars. SpnG, which catalyzes their 9-OH rhamnosylation, is also capable of adding other monosaccharides to the ...

    Spinosyns A and D (spinosad), like many other complex polyketides, are tailored near the end of their biosyntheses through the addition of sugars. SpnG, which catalyzes their 9-OH rhamnosylation, is also capable of adding other monosaccharides to the spinosyn aglycone (AGL) from TDP-sugars; however, the substitution of UDP-D-glucose for TDP-D-glucose as the donor substrate is known to result in a >60000-fold reduction in k(cat). Here, we report the structure of SpnG at 1.65 Å resolution, SpnG bound to TDP at 1.86 Å resolution, and SpnG bound to AGL at 1.70 Å resolution. The SpnG-TDP complex reveals how SpnG employs N202 to discriminate between TDP- and UDP-sugars. A conformational change of several residues in the active site is promoted by the binding of TDP. The SpnG-AGL complex shows that the binding of AGL is mediated via hydrophobic interactions and that H13, the potential catalytic base, is within 3 Å of the nucleophilic 9-OH group of AGL. A model for the Michaelis complex was constructed to reveal the features that allow SpnG to transfer diverse sugars; it also revealed that the rhamnosyl moiety is in a skew-boat conformation during the transfer reaction.


    Organizational Affiliation

    Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NDP-rhamnosyltransferase
A, B
387Saccharopolyspora spinosaMutation(s): 0 
Gene Names: spnG
Find proteins for Q9ALM8 (Saccharopolyspora spinosa)
Go to UniProtKB:  Q9ALM8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TYD
Query on TYD

Download SDF File 
Download CCD File 
A, B
THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
B
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.232 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 54.152α = 81.63
b = 57.629β = 73.79
c = 68.203γ = 85.74
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data scaling
PHASERphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-02-29
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Structure summary