9GN4 image
Entry Detail
PDB ID:
9GN4
Keywords:
Title:
Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii. Y7F/D72N mutant with cytidine
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2024-08-30
Release Date:
2024-12-25
Method Details:
Experimental Method:
Resolution:
2.48 Å
R-Value Free:
0.18
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
I 21 3
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Nucleoside deoxyribosyltransferase
Mutations:Y7F, D72N
Chain IDs:A, B
Chain Length:157
Number of Molecules:2
Biological Source:Lactobacillus leichmannii
Ligand Molecules
Primary Citation
Biocatalytic synthesis of ribonucleoside analogues using nucleoside transglycosylase-2.
Chem Sci 16 1302 1307 (2025)
PMID: 39691463 DOI: 10.1039/d4sc07521h

Abstact

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 (LlNDT-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.

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