› 1xjn

X-ray diffraction
2.25Å resolution

Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP-CDP complex

Released:
DOI: 10.2210/pdb1xjn/pdb
PDB entry 1xjn coloured by chain, front view.
PDB entry 1xjn coloured by chain, side view.
PDB entry 1xjn coloured by chain, top view.
Source organism: Thermotoga maritima
Primary publication:
Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase.
Larsson KM, Jordan A, Eliasson R, Reichard P, Logan DT, Nordlund P
Nat Struct Mol Biol 11 1142-9 (2004)
PMID: 15475969

Function and Biology Details

Reaction catalysed: 
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128506 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Vitamin B12-dependent ribonucleotide reductase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 644 amino acids
Theoretical weight: 73.37 KDa
Source organism: Thermotoga maritima
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O33839 (Residues: 1-644; Coverage: 78%)
Gene name: nrdJ
Sequence domains:
Structure domains: Anaerobic Ribonucleotide-triphosphate Reductase Large Chain

Ligands and Environments

3 bound ligands:
Ligand CDP 4 x CDP
Ligand DTP 4 x DTP
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: P21
Unit cell:
a: 105.97Å b: 123.83Å c: 117.41Å
α: 90° β: 104.02° γ: 90°
R-values:
R R work R free
0.193 0.19 0.254
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

Ribonucleotide reductases.
Nordlund et al. (2006)
9 more

3 mentions without citation

The class III ribonucleotide reductase from Neisseria bacilliformis can utilize thioredoxin as a reductant.
Wei et al. (2014)
2 more