› 4yoy

X-ray diffraction
1.95Å resolution

Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 in complex with poly-dT and Mg2+ ion

Released:
DOI: 10.2210/pdb4yoy/pdb
PDB entry 4yoy coloured by chain, front view.
PDB entry 4yoy coloured by chain, side view.
PDB entry 4yoy coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for substrate recognition and processive cleavage mechanisms of the trimeric exonuclease PhoExo I.
Miyazono K, Ishino S, Tsutsumi K, Ito T, Ishino Y, Tanokura M
Nucleic Acids Res 43 7122-36 (2015)
PMID: 26138487

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-100321 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DUF4152 family protein Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 233 amino acids
Theoretical weight: 26.22 KDa
Source organism: Pyrococcus horikoshii
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A060P168 (Residues: 1-229; Coverage: 100%)
Gene name: HA331_07515
Sequence domains: Protein of unknown function (DUF4152)
Structure domains: Protein of unknown function DUF4152
5'-D(*TP*TP*TP*TP*TP*TP*T)-3' Chains: B, D, F
Molecule details ›
Chains: B, D, F
Length: 7 nucleotides
Theoretical weight: 2.08 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P212121
Unit cell:
a: 94.878Å b: 94.891Å c: 106.457Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.18 0.204
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 citation in other articles

Structure and Mechanism of a Cyclic Trinucleotide-Activated Bacterial Endonuclease Mediating Bacteriophage Immunity.
Lau et al. (2020)
2 more

1 mention without citation

Structural basis for substrate recognition and processive cleavage mechanisms of the trimeric exonuclease PhoExo I.
Miyazono et al. (2015)