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PDBsum entry 4hx9

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protein ligands Protein-protein interface(s) links
Transferase PDB id
4hx9
Jmol
Contents
Protein chains
(+ 2 more) 156 a.a.
Ligands
SO4 ×14
PG4 ×6
Waters ×209
PDB id:
4hx9
Name: Transferase
Title: Designed phosphodeoxyribosyltransferase
Structure: Nucleoside deoxyribosyltransferase. Chain: a, b, e, f, c, d, g, h. Synonym: n-deoxyribosyltransferase. Engineered: yes. Mutation: yes
Source: Lactobacillus leichmannii. Organism_taxid: 28039. Gene: ntd. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.68Å     R-factor:   0.198     R-free:   0.250
Authors: P.A.Kaminski,G.Labesse
Key ref: P.A.Kaminski and G.Labesse (2013). Phosphodeoxyribosyltransferases, designed enzymes for deoxyribonucleotides synthesis. J Biol Chem, 288, 6534-6541. PubMed id: 23325804 DOI: 10.1074/jbc.M112.446492
Date:
09-Nov-12     Release date:   16-Jan-13    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9R5V5  (NTD_LACLE) -  Nucleoside deoxyribosyltransferase
Seq:
Struc:
157 a.a.
156 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.4.2.6  - Nucleoside deoxyribosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-deoxy-D-ribosyl-base1 + base2 = 2-deoxy-D-ribosyl-base2 + base1
2-deoxy-D-ribosyl-base(1)
+ base(2)
= 2-deoxy-D-ribosyl-base(2)
+ base(1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleotide salvage   3 terms 
  Biochemical function     transferase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1074/jbc.M112.446492 J Biol Chem 288:6534-6541 (2013)
PubMed id: 23325804  
 
 
Phosphodeoxyribosyltransferases, designed enzymes for deoxyribonucleotides synthesis.
P.A.Kaminski, G.Labesse.
 
  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.