9F08 | pdb_00009f08

Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii. Covalent complex with 2-deoxyribose.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 
    0.228 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.204 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Literature

Gram-scale enzymatic synthesis of 2'-deoxyribonucleoside analogues using nucleoside transglycosylase-2.

Salihovic, A.Ascham, A.Taladriz-Sender, A.Bryson, S.Withers, J.M.McKean, I.J.W.Hoskisson, P.A.Grogan, G.Burley, G.A.

(2024) Chem Sci 15: 15399-15407

  • DOI: https://doi.org/10.1039/d4sc04938a
  • Primary Citation Related Structures: 
    9EZK, 9F08, 9F09

  • PubMed Abstract: 

    Nucleosides are pervasive building blocks that are found throughout nature and used extensively in medicinal chemistry and biotechnology. However, the preparation of base-modified analogues using conventional synthetic methodology poses challenges in scale-up and purification. In this work, an integrated approach involving structural analysis, screening and reaction optimization, is established to prepare 2'-deoxyribonucleoside analogues catalysed by the type II nucleoside 2'-deoxyribosyltransferase from Lactobacillus leichmannii ( Ll NDT-2). Structural analysis in combination with substrate profiling, identified the constraints on pyrimidine and purine acceptor bases by Ll NDT2. A solvent screen identifies pure water as a suitable solvent for the preparation of high value purine and pyrimidine 2'-deoxyribonucleoside analogues on a gram scale under optimized reaction conditions. This approach provides the basis to establish a convergent, step-efficient chemoenzymatic platform for the preparation of high value 2'-deoxyribonucleosides.


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

Macromolecule Content 

  • Total Structure Weight: 36.46 kDa 
  • Atom Count: 2,575 
  • Modeled Residue Count: 314 
  • Deposited Residue Count: 314 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleoside deoxyribosyltransferase
A, B
157Lactobacillus leichmanniiMutation(s): 0 
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: 2.37 Å
  • R-Value Free:  0.228 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.204 (DCC) 
Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.461α = 90
b = 148.461β = 90
c = 148.461γ = 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: 2024-12-04
    Type: Initial release