› 8q1k

X-ray diffraction
1.51Å resolution

Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation

Released:
DOI: 10.2210/pdb8q1k/pdb
PDB entry 8q1k coloured by chain, front view.
PDB entry 8q1k coloured by chain, side view.
PDB entry 8q1k coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation.
Roske Y, Cappel C, Cremer N, Hoffmann P, Koudelka T, Tholey A, Heinemann U, Daumke O, Damme M
OpenAccess logo Nucleic Acids Res (2023)
PMID: 37994783

Function and Biology Details

Reaction catalysed: 
Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 3'-phosphates
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-236367 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (4 distinct):
5'-3' exonuclease PLD3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 422 amino acids
Theoretical weight: 46.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8IV08 (Residues: 72-490; Coverage: 86%)
Gene name: PLD3
Sequence domains: PLD-like domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN, BMA
Carbohydrate polymer
3 bound ligands:
Ligand EDO 7 x EDO
Ligand PO4 8 x PO4
Ligand MN 4 x MN
1 modified residue:
Ligand OCS 2 x OCS

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P21
Unit cell:
a: 60.251Å b: 115.304Å c: 101.082Å
α: 90° β: 106.64° γ: 90°
R-values:
R R work R free
0.154 0.154 0.186
Expression system: Escherichia coli

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Citations

1 mention without citation

Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation.
Roske et al. (2024)