9GN2 | pdb_00009gn2

Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii. Complex with ribose and cytosine

• PDB DOI: https://doi.org/10.2210/pdb9GN2/pdb

• Classification: TRANSFERASE
• Organism(s): Lactobacillus leichmannii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-30 Released: 2024-12-25 
• Deposition Author(s): Ascham, A., Salihovic, A., Burley, G., Grogan, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.214 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.192 (DCC) 

Starting Model: experimental

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.

(2025) Chem Sci 16: 1302-1307

• PubMed: 39691463 
• DOI: https://doi.org/10.1039/d4sc07521h
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Pure & Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK [e-mail].
Strathclyde Centre for Molecular Bioscience, University of Strathclyde Glasgow UK.
Department of Chemistry, University of York Heslington York YO10 5DD UK [e-mail].
Department of Chemistry, Durham University South Road Durham DH1 3LE UK.
Strathclyde Institute of Pharmacy & Biomedical Sciences, University of Strathclyde 161 Cathedral Street Glasgow G4 0RE UK.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.46 kDa 
• Atom Count: 2,613 
• Modeled Residue Count: 314 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside deoxyribosyltransferase	A, B	157	Lactobacillus leichmannii	Mutation(s): 0  Gene Names: ntd EC: 2.4.2.6
UniProt
Find proteins for Q9R5V5 (Lactobacillus leichmannii) Explore Q9R5V5  Go to UniProtKB:  Q9R5V5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RIB (Subject of Investigation/LOI)	D [auth A]	alpha-D-ribofuranose C5 H10 O5 HMFHBZSHGGEWLO-AIHAYLRMSA-N
CYT (Subject of Investigation/LOI)	C [auth A]	6-AMINOPYRIMIDIN-2(1H)-ONE C4 H5 N3 O OPTASPLRGRRNAP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.214 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.192 (DCC) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.981	α = 90
b = 148.981	β = 90
c = 148.981	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Ascham, A., Salihovic, A., Burley, G., Grogan, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release
  
• Version 1.1: 2025-01-01
  Changes: Database references
• Version 1.2: 2025-01-29
  Changes: Database references