› 6gfl

X-ray diffraction
2.48Å resolution

Crystal structure of the Escherichia coli nucleosidase PpnN (apo form)

Released:
DOI: 10.2210/pdb6gfl/pdb
PDB entry 6gfl coloured by chain, front view.
PDB entry 6gfl coloured by chain, side view.
PDB entry 6gfl coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
(p)ppGpp Regulates a Bacterial Nucleosidase by an Allosteric Two-Domain Switch.
Zhang YE, Bærentsen RL, Fuhrer T, Sauer U, Gerdes K, Brodersen DE
Mol Cell 74 1239-1249.e4 (2019)
PMID: 31023582

Function and Biology Details

Reactions catalysed: 
A pyrimidine 5'-nucleotide + H(2)O = D-ribose 5-phosphate + a pyrimidine base
AMP + H(2)O = D-ribose 5-phosphate + adenine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142373 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 474 amino acids
Theoretical weight: 53.24 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0ADR8 (Residues: 2-454; Coverage: 100%)
Gene names: JW2766, b2795, ppnN, ygdH
Sequence domains:
Structure domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P21212
Unit cell:
a: 94.17Å b: 101.08Å c: 112.29Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.212 0.269
Expression system: Escherichia coli BL21(DE3)

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Citations

6 review citations

The stringent response and physiological roles of (pp)pGpp in bacteria.
Irving et al. (2021)
5 more