› 4hx9

X-ray diffraction
2.68Å resolution

Designed Phosphodeoxyribosyltransferase

Released:
DOI: 10.2210/pdb4hx9/pdb
PDB entry 4hx9 coloured by chain, front view.
PDB entry 4hx9 coloured by chain, side view.
PDB entry 4hx9 coloured by chain, top view.
Source organism: Lactobacillus leichmannii
Primary publication:
Phosphodeoxyribosyltransferases, designed enzymes for deoxyribonucleotides synthesis.
Kaminski PA, Labesse G
J Biol Chem 288 6534-41 (2013)
PMID: 23325804

Function and Biology Details

Reaction catalysed: 
2-deoxy-D-ribosyl-base(1) + base(2) = 2-deoxy-D-ribosyl-base(2) + base(1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193111 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside deoxyribosyltransferase Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 157 amino acids
Theoretical weight: 18.02 KDa
Source organism: Lactobacillus leichmannii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9R5V5 (Residues: 1-157; Coverage: 100%)
Gene name: ntd
Sequence domains: Nucleoside 2-deoxyribosyltransferase
Structure domains: Rossmann fold

Ligands and Environments

2 bound ligands:
Ligand SO4 14 x SO4
Ligand PG4 6 x PG4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: I213
Unit cell:
a: 218.454Å b: 218.454Å c: 218.454Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.195 0.25
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Biocatalytic approaches applied to the synthesis of nucleoside prodrugs.
Iglesias et al. (2015)
5 other articles

1 mention without citation

Phosphodeoxyribosyltransferases, designed enzymes for deoxyribonucleotides synthesis.
Kaminski et al. (2013)