4AMB

Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.227 

Starting Model: experimental
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Literature

Crystal Structure of the Glycosyltransferase Snogd from the Biosynthetic Pathway of the Nogalamycin in Streptomyces Nogalater.

Claesson, M.Siitonen, V.Dobritzsch, D.Metsa-Ketela, M.Schneider, G.

(2012) FEBS J 279: 3251

  • DOI: https://doi.org/10.1111/j.1742-4658.2012.08711.x
  • Primary Citation of Related Structures:  
    4AMB, 4AMG, 4AN4

  • PubMed Abstract: 

    The glycosyltransferase SnogD from Streptomyces nogalater transfers a nogalamine moiety to the metabolic intermediate 3',4'-demethoxynogalose-1-hydroxynogalamycinone during the final steps of biosynthesis of the aromatic polyketide nogalamycin. The crystal structure of recombinant SnogD, as an apo-enzyme and with a bound nucleotide, 2-deoxyuridine-5'-diphosphate, was determined to 2.6 Å resolution. Reductive methylation of SnogD was crucial for reproducible preparation of diffraction quality crystals due to creation of an additional intermolecular salt bridge between methylated lysine residue Lys384 and Glu374* from an adjacent molecule in the crystal lattice. SnogD is a dimer both in solution and in the crystal, and the enzyme subunit displays a fold characteristic of the GT-B family of glycosyltransferases. Binding of the nucleotide is associated with rearrangement of two active-site loops. Site-directed mutagenesis shows that two active-site histidine residues, His25 and His301, are critical for the glycosyltransferase activities of SnogD both in vivo and in vitro. The crystal structures and the functional data are consistent with a role for His301 in binding of the diphosphate group of the sugar donor substrate, and a function of His25 as a catalytic base in the glycosyl transfer reaction.


  • Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SNOGD
A, B
400Streptomyces nogalaterMutation(s): 0 
UniProt
Find proteins for Q9RN61 (Streptomyces nogalater)
Explore Q9RN61 
Go to UniProtKB:  Q9RN61
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RN61
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DUD
Query on DUD

Download Ideal Coordinates CCD File 
C [auth B]DEOXYURIDINE-5'-DIPHOSPHATE
C9 H14 N2 O11 P2
QHWZTVCCBMIIKE-SHYZEUOFSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.911α = 90
b = 170.955β = 90
c = 69.427γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description