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


Ligand Structure Quality Assessment 

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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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 2DRClick on this verticalbar to view details

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