› 4ojx

X-ray diffraction
1.31Å resolution

crystal structure of yeast phosphodiesterase-1 in complex with GMP

Released:
DOI: 10.2210/pdb4ojx/pdb
PDB entry 4ojx coloured by chain, front view.
PDB entry 4ojx coloured by chain, side view.
PDB entry 4ojx coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cyclic adenosine and guanosine 3',5'-monophosphate.
Tian Y, Cui W, Huang M, Robinson H, Wan Y, Wang Y, Ke H
Biochemistry 53 4938-45 (2014)
PMID: 25050706

Function and Biology Details

Reaction catalysed: 
Nucleoside 3',5'-cyclic phosphate + H(2)O = nucleoside 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149630 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3',5'-cyclic-nucleotide phosphodiesterase 1 Chain: A
Molecule details ›
Chain: A
Length: 369 amino acids
Theoretical weight: 42.07 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P22434 (Residues: 1-369; Coverage: 100%)
Gene names: NRB369, PDE1, YGL248W
Sequence domains: cAMP phosphodiesterases class-II

Ligands and Environments

3 bound ligands:
Ligand MPD 1 x MPD
Ligand 5GP 1 x 5GP
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: C2221
Unit cell:
a: 73.674Å b: 85.162Å c: 130.836Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.169 0.168 0.179
Expression system: Escherichia coli BL21

Quick links

Citations

4 review citations

In Search of Enzymes with a Role in 3', 5'-Cyclic Guanosine Monophosphate Metabolism in Plants.
Gross et al. (2016)
3 more

1 mention without citation

Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cyclic adenosine and guanosine 3',5'-monophosphate.
Tian et al. (2014)