› 1f8y

X-ray diffraction
2.4Å resolution

CRYSTAL STRUCTURE ANALYSIS OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE COMPLEXED WITH 5-METHYL-2'-DEOXYPSEUDOURIDINE

Released:
DOI: 10.2210/pdb1f8y/pdb
PDB entry 1f8y coloured by chain, front view.
PDB entry 1f8y coloured by chain, side view.
PDB entry 1f8y coloured by chain, top view.
Source organism: Lactobacillus leichmannii
Primary publication:
Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site.
Armstrong SR, Cook WJ, Short SA, Ealick SE
Structure 4 97-107 (1996)
PMID: 8805514

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 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
Molecule details ›
Chains: A, B
Length: 157 amino acids
Theoretical weight: 18.1 KDa
Source organism: Lactobacillus leichmannii
UniProt:
  • Canonical: Q9R5V5 (Residues: 1-157; Coverage: 100%)
Gene name: ntd
Sequence domains: Nucleoside 2-deoxyribosyltransferase
Structure domains: Rossmann fold

Ligands and Environments

1 bound ligand:
Ligand 5MD 2 x 5MD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: I213
Unit cell:
a: 149.6Å b: 149.6Å c: 149.6Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.16 0.218

Quick links

Citations

3 review citations

Nucleotide metabolism and its control in lactic acid bacteria.
Kilstrup et al. (2005)
2 more

5 mentions without citation

The SARM1 Toll/Interleukin-1 Receptor Domain Possesses Intrinsic NAD+ Cleavage Activity that Promotes Pathological Axonal Degeneration.
Essuman et al. (2017)
4 more