› 2xsq

X-ray diffraction
1.72Å resolution

Crystal structure of human Nudix motif 16 (NUDT16) in complex with IMP and magnesium

Released:
DOI: 10.2210/pdb2xsq/pdb
PDB entry 2xsq coloured by chain, front view.
PDB entry 2xsq coloured by chain, side view.
PDB entry 2xsq coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Basis for the Specificity of Human NUDT16 and Its Regulation by Inosine Monophosphate.
Trésaugues L, Lundbäck T, Welin M, Flodin S, Nyman T, Silvander C, Gräslund S, Nordlund P
PLoS One 10 e0131507 (2015)
PMID: 26121039

Function and Biology Details

Reactions catalysed: 
5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] + H(2)O = N(7)-methylguanosine 5'-diphosphate + 5'-phospho-[mRNA]
IDP + H(2)O = IMP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188436 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
U8 snoRNA-decapping enzyme Chain: A
Molecule details ›
Chain: A
Length: 217 amino acids
Theoretical weight: 23.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96DE0 (Residues: 1-195; Coverage: 100%)
Gene name: NUDT16
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

3 bound ligands:
Ligand IMP 1 x IMP
Ligand MG 2 x MG
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: F23
Unit cell:
a: 141.583Å b: 141.583Å c: 141.583Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.159 0.181
Expression system: Escherichia coli BL21(DE3)

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Citations

4 review citations

The complex enzymology of mRNA decapping: Enzymes of four classes cleave pyrophosphate bonds.
Kramer et al. (2019)
3 more

10 mentions without citation

Nudix hydrolases degrade protein-conjugated ADP-ribose.
Daniels et al. (2015)
9 more