› 2pau

X-ray diffraction
2.1Å resolution

Crystal structure of the 5'-deoxynucleotidase YfbR mutant E72A complexed with Co(2+) and dAMP

Released:
DOI: 10.2210/pdb2pau/pdb
PDB entry 2pau coloured by chain, front view.
PDB entry 2pau coloured by chain, side view.
PDB entry 2pau coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli.
Zimmerman MD, Proudfoot M, Yakunin A, Minor W
J Mol Biol 378 215-26 (2008)
PMID: 18353368

Function and Biology Details

Reaction catalysed: 
A 2'-deoxyribonucleoside 5'-monophosphate + H(2)O = a 2'-deoxyribonucleoside + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo hexamer
Assembly name:
PDBe Complex ID:
PDB-CPX-160095 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
5'-deoxynucleotidase YfbR Chains: A, B
Molecule details ›
Chains: A, B
Length: 201 amino acids
Theoretical weight: 22.87 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P76491 (Residues: 1-199; Coverage: 100%)
Gene names: JW2288, b2291, yfbR
Sequence domains: HD domain
Structure domains: Hypothetical protein af1432

Ligands and Environments

3 bound ligands:
Ligand CO 2 x CO
Ligand D5M 2 x D5M
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: R3
Unit cell:
a: 135.595Å b: 135.595Å c: 54.936Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.196 0.193 0.26
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Aicardi-Goutieres syndrome and related phenotypes: linking nucleic acid metabolism with autoimmunity.
Crow et al. (2009)
4 more

4 mentions without citation

Divergence and convergence in enzyme evolution.
Galperin et al. (2012)
3 more