› 5uli

X-ray diffraction
2.1Å resolution

Crystal Structure of mouse DXO in complex with (3'-NADP)+ and calcium ion

Released:
DOI: 10.2210/pdb5uli/pdb
PDB entry 5uli coloured by chain, front view.
PDB entry 5uli coloured by chain, side view.
PDB entry 5uli coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
5' End Nicotinamide Adenine Dinucleotide Cap in Human Cells Promotes RNA Decay through DXO-Mediated deNADding.
Jiao X, Doamekpor SK, Bird JG, Nickels BE, Tong L, Hart RP, Kiledjian M
Cell 168 1015-1027.e10 (2017)
PMID: 28283058

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130692 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Decapping and exoribonuclease protein Chain: A
Molecule details ›
Chain: A
Length: 378 amino acids
Theoretical weight: 43.13 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O70348 (Residues: 27-384; Coverage: 90%)
Gene names: Dom3z, Dxo, Ng6
Sequence domains: RAI1 like PD-(D/E)XK nuclease

Ligands and Environments

2 bound ligands:
Ligand CA 1 x CA
Ligand 0WD 1 x 0WD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 49.867Å b: 87.678Å c: 53.158Å
α: 90° β: 113.02° γ: 90°
R-values:
R R work R free
0.165 0.161 0.208
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

36 review citations

NAD+ metabolism: pathophysiologic mechanisms and therapeutic potential.
Xie et al. (2020)
35 more

3 mentions without citation

5' End Nicotinamide Adenine Dinucleotide Cap in Human Cells Promotes RNA Decay through DXO-Mediated deNADding.
Jiao et al. (2017)
2 more