› 2yph

X-ray diffraction
2.1Å resolution

Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation H230S, crystallized with 2',3-(RP)- cyclic-AMPS

Released:
DOI: 10.2210/pdb2yph/pdb
PDB entry 2yph coloured by chain, front view.
PDB entry 2yph coloured by chain, side view.
PDB entry 2yph coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Crystallographic analysis of the reaction cycle of 2',3'-cyclic nucleotide 3'-phosphodiesterase, a unique member of the 2H phosphoesterase family.
Myllykoski M, Raasakka A, Lehtimäki M, Han H, Kursula I, Kursula P
J Mol Biol 425 4307-22 (2013)
PMID: 23831225

Function and Biology Details

Reaction catalysed: 
Nucleoside 2',3'-cyclic phosphate + H(2)O = nucleoside 2'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147689 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2',3'-cyclic-nucleotide 3'-phosphodiesterase Chain: A
Molecule details ›
Chain: A
Length: 221 amino acids
Theoretical weight: 24.24 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P16330 (Residues: 179-398; Coverage: 52%)
Gene names: Cnp, Cnp1
Sequence domains: 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase)
Structure domains: 2',3'-cyclic nucleotide 3'-phosphodiesterase superfamily

Ligands and Environments

3 bound ligands:
Ligand ACT 1 x ACT
Ligand CL 1 x CL
Ligand QQY 1 x QQY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I911-2
Spacegroup: P212121
Unit cell:
a: 40.63Å b: 47.53Å c: 107.55Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.23 0.289
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Generation of 2',3'-Cyclic Phosphate-Containing RNAs as a Hidden Layer of the Transcriptome.
Shigematsu et al. (2018)
4 more

1 mention without citation

Crystallographic analysis of the reaction cycle of 2',3'-cyclic nucleotide 3'-phosphodiesterase, a unique member of the 2H phosphoesterase family.
Myllykoski et al. (2013)