› 1ptw

X-ray diffraction
2.3Å resolution

The Crystal Structure of AMP-Bound PDE4 Suggests a Mechanism for Phosphodiesterase Catalysis

Released:
DOI: 10.2210/pdb1ptw/pdb
PDB entry 1ptw coloured by chain, front view.
PDB entry 1ptw coloured by chain, side view.
PDB entry 1ptw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The crystal structure of AMP-bound PDE4 suggests a mechanism for phosphodiesterase catalysis.
Huai Q, Colicelli J, Ke H
Biochemistry 42 13220-6 (2003)
PMID: 14609333

Function and Biology Details

Reaction catalysed: 
Adenosine 3',5'-cyclic phosphate + H(2)O = adenosine 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170656 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3',5'-cyclic-AMP phosphodiesterase 4D Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 360 amino acids
Theoretical weight: 41.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q08499 (Residues: 381-740; Coverage: 45%)
Gene names: DPDE3, PDE4D
Sequence domains: 3'5'-cyclic nucleotide phosphodiesterase
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand AMP 4 x AMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: P212121
Unit cell:
a: 99.207Å b: 111.229Å c: 159.65Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.229 0.274
Expression system: Escherichia coli BL21

Quick links

Citations

12 review citations

Biochemistry and physiology of cyclic nucleotide phosphodiesterases: essential components in cyclic nucleotide signaling.
Conti et al. (2007)
11 more

3 mentions without citation

Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility.
Loving et al. (2014)
2 more