› 5w6x

X-ray diffraction
2.1Å resolution

Crystal structure of the HsNUDT16 in complex with Mg+2 and ADP-ribose

Released:
DOI: 10.2210/pdb5w6x/pdb
PDB entry 5w6x coloured by chain, front view.
PDB entry 5w6x coloured by chain, side view.
PDB entry 5w6x coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural analyses of NudT16-ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins.
Thirawatananond P, McPherson RL, Malhi J, Nathan S, Lambrecht MJ, Brichacek M, Hergenrother PJ, Leung AKL, Gabelli SB
Sci Rep 9 5940 (2019)
PMID: 30976021

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 Chains: A, B
Molecule details ›
Chains: A, B
Length: 195 amino acids
Theoretical weight: 21.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96DE0 (Residues: 1-195; Coverage: 100%)
Gene name: NUDT16
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

4 bound ligands:
Ligand APR 2 x APR
Ligand MG 4 x MG
Ligand ACY 2 x ACY
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E DW
Spacegroup: C2
Unit cell:
a: 113.755Å b: 46.319Å c: 74.238Å
α: 90° β: 107.65° γ: 90°
R-values:
R R work R free
0.183 0.181 0.238
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Recent insights into noncanonical 5' capping and decapping of RNA.
Doamekpor et al. (2022)
1 more

3 mentions without citation

Structural analyses of NudT16-ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins.
Thirawatananond et al. (2019)
2 more