4LEI | pdb_00004lei

Spinosyn Forosaminyltransferase SpnP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 
    0.314 (Depositor), 0.307 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

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This is version 1.1 of the entry. See complete history

Literature

Structural studies of the spinosyn forosaminyltransferase, SpnP.

Isiorho, E.A.Jeon, B.S.Kim, N.H.Liu, H.W.Keatinge-Clay, A.T.

(2014) Biochemistry 53: 4292-4301

  • DOI: https://doi.org/10.1021/bi5003629
  • Primary Citation Related Structures: 
    4LEI

  • PubMed Abstract: 

    Spinosyns A and D (spinosad) are complex polyketide natural products biosynthesized through the cooperation of a modular polyketide synthase and several tailoring enzymes. SpnP catalyzes the final tailoring step, transferring forosamine from a TDP-D-forosamine donor substrate to a spinosyn pseudoaglycone acceptor substrate. Sequence analysis indicated that SpnP belongs to a small group of glycosyltransferases (GTs) that require an auxiliary protein for activation. However, unlike other GTs in this subgroup, no putative auxiliary protein gene could be located in the biosynthetic gene cluster. To learn more about SpnP, the structures of SpnP and its complex with TDP were determined to 2.50 and 3.15 Å resolution, respectively. Binding of TDP causes the reordering of several residues in the donor substrate pocket. SpnP possesses a structural feature that has only been previously observed in the related glycosyltransferase EryCIII, in which it mediates association with the auxiliary protein EryCII. This motif, H-X-R-X5-D-X5-R-X12-20-D-P-X3-W-L-X12-18-E-X4-G, may be predictive of glycosyltransferases that interact with an auxiliary protein. A reverse glycosyl transfer assay demonstrated that SpnP possesses measurable activity in the absence of an auxiliary protein. Our data suggest that SpnP can bind its donor substrate by itself but that the glycosyl transfer reaction is facilitated by an auxiliary protein that aids in the correct folding of a flexible loop surrounding the pseudoaglycone acceptor substrate-binding pocket.


  • Organizational Affiliation
    • Division of Medicinal Chemistry, College of Pharmacy, and ‡Department of Chemistry and Biochemistry, The University of Texas at Austin , Austin, Texas 78712, United States.

Macromolecule Content 

  • Total Structure Weight: 101.81 kDa 
  • Atom Count: 5,958 
  • Modeled Residue Count: 748 
  • Deposited Residue Count: 910 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NDP-forosamyltransferase
A, B
455Saccharopolyspora spinosaMutation(s): 0 
Gene Names: spnP
UniProt
Find proteins for Q9ALN7 (Saccharopolyspora spinosa)
Explore Q9ALN7 
Go to UniProtKB:  Q9ALN7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ALN7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free:  0.314 (Depositor), 0.307 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.369α = 90
b = 162.369β = 90
c = 81.279γ = 90
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: 2014-12-10
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations