Biological Assembly 1  

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 167491.25 
• Atom Count: 10802 
• Residue Count: 1440 
• Unique protein chains: 1

1PTW

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

• DOI: 10.2210/pdb1PTW/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21


• Deposited: 2003-06-23 Released: 2003-11-11 
• Deposition Author(s): Huai, Q., Colicelli, J., Ke, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.274 
• R-Value Work: 0.229 

Literature

The crystal structure of AMP-bound PDE4 suggests a mechanism for phosphodiesterase catalysis

Huai, Q., Colicelli, J., Ke, H.

(2003) Biochemistry 42: 13220-13226

• PubMed: 14609333 
• DOI: 10.1021/bi034653e


• PubMed Abstract: 
  

Cyclic nucleotide phosphodiesterases (PDEs) regulate the intracellular concentrations of cyclic 3',5'-adenosine and guanosine monophosphates (cAMP and cGMP, respectively) by hydrolyzing them to AMP and GMP, respectively. Family-selective inhibitors of PDEs have been studied for treatment of various human diseases. However, the catalytic mechanism of cyclic nucleotide hydrolysis by PDEs has remained unclear. We determined the crystal structure of the human PDE4D2 catalytic domain in complex with AMP at 2.4 A resolution. In this structure, two divalent metal ions simultaneously interact with the phosphate group of AMP, implying a binuclear catalysis. In addition, the structure suggested that a hydroxide ion or a water bridging two metal ions may serve as the nucleophile for the hydrolysis of the cAMP phosphodiester bond.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, North Carolina 27599-7260, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
cAMP-specific phosphodiesterase PDE4D2	A, B, C, D	360	Homo sapiens	Mutation(s): 0  Gene Names: PDE4D (DPDE3) EC: 3.1.4.53
Find proteins for Q08499 (Homo sapiens) Go to Gene View: PDE4D Go to UniProtKB:  Q08499

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B, C, D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
AMP	A, B, C, D	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.274 
• R-Value Work: 0.229 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 99.207	α = 90.00
b = 111.229	β = 90.00
c = 159.650	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
AMoRE	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-06-23 
• Released Date: 2003-11-11 
• Deposition Author(s): Huai, Q., Colicelli, J., Ke, H.

Revision History 

• Version 1.0: 2003-11-11
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance