› 6ebp

X-ray diffraction
1.59Å resolution

Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit from Aerococcus urinae in Activated Form

Released:
DOI: 10.2210/pdb6ebp/pdb
PDB entry 6ebp coloured by chain, front view.
PDB entry 6ebp coloured by chain, side view.
PDB entry 6ebp coloured by chain, top view.
Source organism: Aerococcus sp. Group 1
Primary publication:
Metal-free class Ie ribonucleotide reductase from pathogens initiates catalysis with a tyrosine-derived dihydroxyphenylalanine radical.
Blaesi EJ, Palowitch GM, Hu K, Kim AJ, Rose HR, Alapati R, Lougee MG, Kim HJ, Taguchi AT, Tan KO, Laremore TN, Griffin RG, Krebs C, Matthews ML, Silakov A, Bollinger JM, Allen BD, Boal AK
OpenAccess logo Proc Natl Acad Sci U S A 115 10022-10027 (2018)
PMID: 30224458

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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123374 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
ribonucleoside-diphosphate reductase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 355 amino acids
Theoretical weight: 40.68 KDa
Source organism: Aerococcus sp. Group 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: F2I8X9 (Residues: 2-337; Coverage: 100%)
Gene name: HMPREF9243_0731
Sequence domains: Ribonucleotide reductase, small chain

Ligands and Environments

2 bound ligands:
Ligand CA 6 x CA
Ligand GOL 4 x GOL
1 modified residue:
Ligand DAH 4 x DAH

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P21
Unit cell:
a: 80.004Å b: 109.417Å c: 83.861Å
α: 90° β: 90.06° γ: 90°
R-values:
R R work R free
0.164 0.163 0.179
Expression system: Escherichia coli BL21(DE3)

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Citations

6 review citations

Ribonucleotide Reductases: Structure, Chemistry, and Metabolism Suggest New Therapeutic Targets.
Greene et al. (2020)
5 more

1 mention without citation

Metal-free class Ie ribonucleotide reductase from pathogens initiates catalysis with a tyrosine-derived dihydroxyphenylalanine radical.
Blaesi et al. (2018)