4HX9

Designed Phosphodeoxyribosyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Phosphodeoxyribosyltransferases, designed enzymes for deoxyribonucleotides synthesis.

Kaminski, P.A.Labesse, G.

(2013) J.Biol.Chem. 288: 6534-6541

  • DOI: 10.1074/jbc.M112.446492

  • PubMed Abstract: 
  • A large number of nucleoside analogues and 2'-deoxynucleoside triphosphates (dNTP) have been synthesized to interfere with DNA metabolism. However, in vivo the concentration and phosphorylation of these analogues are key limiting factors. In this con ...

    A large number of nucleoside analogues and 2'-deoxynucleoside triphosphates (dNTP) have been synthesized to interfere with DNA metabolism. However, in vivo the concentration and phosphorylation of these analogues are key limiting factors. In this context, we designed enzymes to switch nucleobases attached to a deoxyribose monophosphate. Active chimeras were made from two distantly related enzymes: a nucleoside deoxyribosyltransferase from lactobacilli and a 5'-monophosphate-2'-deoxyribonucleoside hydrolase from rat. Then their unprecedented activity was further extended to deoxyribose triphosphate, and in vitro biosyntheses could be successfully performed with several base analogues. These new enzymes provide new tools to synthesize dNTP analogues and to deliver them into cells.


    Organizational Affiliation

    Institut Pasteur, Unité de Chimie et Biocatalyse, CNRS, UMR 3523, 75724 Paris cedex 15, France. pierre-alexandre.kaminski@pasteur.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoside deoxyribosyltransferase
A, B, E, F, C, D, G, H
157Lactobacillus leichmanniiGene Names: ntd
EC: 2.4.2.6
Find proteins for Q9R5V5 (Lactobacillus leichmannii)
Go to UniProtKB:  Q9R5V5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A, B, D, F
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.195 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 218.454α = 90.00
b = 218.454β = 90.00
c = 218.454γ = 90.00
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-02-13
    Type: Database references
  • Version 1.2: 2013-03-20
    Type: Database references