9GN4

Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii. Y7F/D72N mutant with cytidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Biocatalytic synthesis of ribonucleoside analogues using nucleoside transglycosylase-2.

Salihovic, A.Ascham, A.Rosenqvist, P.S.Taladriz-Sender, A.Hoskisson, P.A.Hodgson, D.R.W.Grogan, G.Burley, G.A.

(2024) Chem Sci 

  • DOI: https://doi.org/10.1039/d4sc07521h
  • Primary Citation of Related Structures:  
    9GN2, 9GN4

  • PubMed Abstract: 

    Ribonucleosides are essential building blocks used extensively in antiviral and oligonucleotide therapeutics. A major challenge in the further development of nucleoside analogues for therapeutic applications is access to scalable and environmentally sustainable synthetic strategies. This study uses the type II nucleoside 2'-deoxyribosyltransferase from Lactobacillus leichmannii ( Ll NDT-2) to prepare a suite of ribonucleoside analogues using naturally-occurring uridine and cytidine sugar donors. Crystal structure and mutational analyses are used to define the substrate tolerance of the nucleobase exchange and the 2'-substituent of the nucleoside sugar donor. Nucleobase profiling identified acceptance of both purine and pyrimidine nucleobases. Finally, the scalability of the approach is showcased, enabling the preparation of ribonucleosides on millimolar scales. This biocatalytic strategy opens up opportunities to establish chemoenzymatic routes to prepare nucleoside analogues incorporating 2' modifications that are of therapeutic importance.


  • Organizational Affiliation

    Department of Pure & Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK glenn.burley@strath.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside deoxyribosyltransferase
A, B
157Lactobacillus leichmanniiMutation(s): 2 
Gene Names: ntd
EC: 2.4.2.6
UniProt
Find proteins for Q9R5V5 (Lactobacillus leichmannii)
Explore Q9R5V5 
Go to UniProtKB:  Q9R5V5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9R5V5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.134α = 90
b = 150.134β = 90
c = 150.134γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-01-01
    Changes: Database references