› 1s2d

X-ray diffraction
2.1Å resolution

Purine 2'-Deoxyribosyl complex with arabinoside: Ribosylated Intermediate (AraA)

Released:
DOI: 10.2210/pdb1s2d/pdb
PDB entry 1s2d coloured by chain, front view.
PDB entry 1s2d coloured by chain, side view.
PDB entry 1s2d coloured by chain, top view.
Source organism: Lactobacillus helveticus
Primary publication:
Structures of purine 2'-deoxyribosyltransferase, substrate complexes, and the ribosylated enzyme intermediate at 2.0 A resolution.
Anand R, Kaminski PA, Ealick SE
Biochemistry 43 2384-93 (2004)
PMID: 14992575

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:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:
Structure domain:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-186003 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside 2-deoxyribosyltransferase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 167 amino acids
Theoretical weight: 18.73 KDa
Source organism: Lactobacillus helveticus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8RLY5 (Residues: 1-167; Coverage: 100%)
Gene names: BC335_1936, GDZ32_10450, IMAU30003_01598, LH5_01102, LHEJCM1062_04650, ndtA, ntd_1, ptd
Sequence domains: Nucleoside 2-deoxyribosyltransferase
Structure domains: Rossmann fold

Ligands and Environments

2 bound ligands:
Ligand ADE 3 x ADE
Ligand V3M 3 x V3M
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 8-BM
Spacegroup: P43212
Unit cell:
a: 79.587Å b: 79.587Å c: 184.973Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.229 0.253
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Biocatalytic approaches applied to the synthesis of nucleoside prodrugs.
Iglesias et al. (2015)
1 more

1 mention without citation

Common Structural Patterns in the Maxicircle Divergent Region of Trypanosomatidae.
Gerasimov et al. (2020)