3UYL | pdb_00003uyl

Spinosyn Rhamnosyltransferase SpnG complexed with thymidine diphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.291 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/10.1021/bi201860q
  • Primary Citation Related Structures: 
    3TSA, 3UYK, 3UYL

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 82.92 kDa 
  • Atom Count: 6,014 
  • Modeled Residue Count: 742 
  • Deposited Residue Count: 774 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NDP-rhamnosyltransferase
A, B
387Saccharopolyspora spinosaMutation(s): 0 
Gene Names: spnG
EC: 2.4.1
UniProt
Find proteins for Q9ALM8 (Saccharopolyspora spinosa)
Explore Q9ALM8 
Go to UniProtKB:  Q9ALM8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ALM8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.291 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
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
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-02-29
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary