› 2cvy

X-ray diffraction
2.4Å resolution

Structures of Yeast Ribonucleotide Reductase I

Released:
DOI: 10.2210/pdb2cvy/pdb
PDB entry 2cvy coloured by chain, front view.
PDB entry 2cvy coloured by chain, side view.
PDB entry 2cvy coloured by chain, top view.
Source organisms:
Primary publication:
Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation.
Xu H, Faber C, Uchiki T, Fairman JW, Racca J, Dealwis C
Proc Natl Acad Sci U S A 103 4022-7 (2006)
PMID: 16537479

Function and Biology Details

Reaction catalysed: 
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140829 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ribonucleoside-diphosphate reductase large chain 1 Chain: A
Molecule details ›
Chain: A
Length: 888 amino acids
Theoretical weight: 99.67 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P21524 (Residues: 1-888; Coverage: 100%)
Gene names: CRT7, RIR1, RNR1, SDS12, YER070W
Sequence domains:
Structure domains: Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Ribonucleoside-diphosphate reductase small chain 1 Chain: B
Molecule details ›
Chain: B
Length: 9 amino acids
Theoretical weight: 1.05 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Not provided
UniProt:
  • Canonical: P09938 (Residues: 391-399; Coverage: 2%)
Gene names: CRT6, J1271, RNR2, YJL026W

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand TTP 1 x TTP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH3R
Spacegroup: P21212
Unit cell:
a: 108.062Å b: 117.59Å c: 64.216Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.218 0.263
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

9 review citations

DNA building blocks: keeping control of manufacture.
Hofer et al. (2012)
8 more

1 mention without citation

Structures of eukaryotic ribonucleotide reductase I define gemcitabine diphosphate binding and subunit assembly.
Xu et al. (2006)