4HX9

Designed Phosphodeoxyribosyltransferase

• PDB DOI: https://doi.org/10.2210/pdb4HX9/pdb

• Classification: TRANSFERASE
• Organism(s): Lactobacillus leichmannii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-11-09 Released: 2013-01-16 
• Deposition Author(s): Kaminski, P.A., Labesse, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 0.250 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 

Literature

Phosphodeoxyribosyltransferases, designed enzymes for deoxyribonucleotides synthesis.

Kaminski, P.A., Labesse, G.

(2013) J Biol Chem 288: 6534-6541

• PubMed: 23325804 
• DOI: https://doi.org/10.1074/jbc.M112.446492
• Primary Citation of Related Structures:  
  4HX9


• 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 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. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 146.7 kDa 
• Atom Count: 10,448 
• Modelled Residue Count: 1,245 
• Deposited Residue Count: 1,256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside deoxyribosyltransferase	A, B, C [auth E], D [auth F], E [auth C], F [auth D], G, H	157	Lactobacillus leichmannii	Mutation(s): 5  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
PG4	K [auth A], M [auth B], R [auth F], S [auth F], W [auth D], X [auth D]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4	AA [auth H], BA [auth H], I [auth A], J [auth A], L [auth B], N [auth E], O [auth E], P [auth F], Q [auth F], T [auth C], U [auth D], V [auth D], Y [auth G], Z [auth G]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 0.250 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 
• Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 218.454	α = 90
b = 218.454	β = 90
c = 218.454	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-16 
Deposition Author(s): Kaminski, P.A., Labesse, G.

Revision History  

• Version 1.0: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2013-02-13
  Changes: Database references
• Version 1.2: 2013-03-20
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description