› 8vhu

X-ray diffraction
2.1Å resolution

Crystal structure of dATP bound E. coli class Ia ribonucleotide reductase alpha construct fused with the C-terminal tail of E. coli class Ia beta subunit

Released:
DOI: 10.2210/pdb8vhu/pdb
PDB entry 8vhu coloured by chain, front view.
PDB entry 8vhu coloured by chain, side view.
PDB entry 8vhu coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
How ATP and dATP Act as Molecular Switches to Regulate Enzymatic Activity in the Prototypical Bacterial Class Ia Ribonucleotide Reductase.
Funk MA, Zimanyi CM, Andree GA, Hamilos AE, Drennan CL
Biochemistry (2024)
PMID: 39164005

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-275972 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribonucleoside-diphosphate reductase 1 subunit alpha; Ribonucleoside-diphosphate reductase 1 subunit beta Chains: A, B
Molecule details ›
Chains: A, B
Length: 807 amino acids
Theoretical weight: 90.94 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P00452 (Residues: 1-734; Coverage: 97%)
  • Canonical: P69924 (Residues: 342-376; Coverage: 9%)
Gene names: JW2228, JW2229, b2234, b2235, dnaF, ftsB, nrdA, nrdB
Sequence domains:

Ligands and Environments

5 bound ligands:
Ligand DTP 3 x DTP
Ligand MG 3 x MG
Ligand NA 1 x NA
Ligand CL 6 x CL
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 88.214Å b: 111.207Å c: 209.701Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.159 0.192
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Analysis of insertions and extensions in the functional evolution of the ribonucleotide reductase family.
Burnim et al. (2022)
1 more