PDBsum entry: 1mkd

Hydrolase

PDB id: 1mkd

Contents

Protein chains

(+ 6 more) 328 a.a. *

Ligands

ZAR ×12

Metals

_ZN ×12

_MG ×12

Waters ×12

* Residue conservation analysis

PDB id:

1mkd

Name:

Hydrolase

Title:

Crystal structure of pde4d catalytic domain and zardaverine complex

Structure:

Phosphodiesterase 4d. Chain: a, b, c, d, e, f, g, h, i, j, k, l. Fragment: catalytic domain. Synonym: camp-specific 3',5'-cyclic phosphodiesterase 4d. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PQS)

Resolution:

2.90Å R-factor: 0.245 R-free: 0.260

Authors:

M.E.Lee,J.Markowitz,J.-O.Lee,H.Lee

Key ref:

M.E.Lee et al. (2002). Crystal structure of phosphodiesterase 4D and inhibitor complex(1). FEBS Lett, 530, 53-58. PubMed id: 12387865 DOI: 10.1016/S0014-5793(02)03396-3

Date:

29-Aug-02 Release date: 01-Mar-03

Protein chains

Q08499  (PDE4D_HUMAN) -  cAMP-specific 3',5'-cyclic phosphodiesterase 4D

Seq: 809 a.a.

Struc: 328 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.1.4.17 - 3',5'-cyclic-nucleotide phosphodiesterase.
• Reaction: Nucleoside 3',5'-cyclic phosphate + H₂O = nucleoside 5'-phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: signal transduction (1 term)
• Biochemical function: catalytic activity (2 terms)

Added reference

DOI no: 10.1016/S0014-5793(02)03396-3

FEBS Lett 530:53-58 (2002)

PubMed id: 12387865

Crystal structure of phosphodiesterase 4D and inhibitor complex(1).

M.E.Lee, J.Markowitz, J.O.Lee, H.Lee.

ABSTRACT

Cyclic nucleotide phosphodiesterases (PDEs) regulate physiological processes by degrading intracellular second messengers, adenosine-3',5'-cyclic phosphate or guanosine-3',5'-cyclic phosphate. The first crystal structure of PDE4D catalytic domain and a bound inhibitor, zardaverine, was determined. Zardaverine binds to a highly conserved pocket that includes the catalytic metal binding site. Zardaverine fills only a portion of the active site pocket. More selective PDE4 inhibitors including rolipram, cilomilast and roflumilast have additional functional groups that can utilize the remaining empty space for increased binding energy and selectivity. In the crystal structure, the catalytic domain of PDE4D possesses an extensive dimerization interface containing residues that are highly conserved in PDE1, 3, 4, 8 and 9. Mutations of R358D or D322R among these interface residues prohibit dimerization of the PDE4D catalytic domain in solution.

Selected figure(s)

Figure 2.
Fig. 2. Dialkoxyphenyl containing PDE4 inhibitors [4, 6, 15, 16, 23, 24 and 25]. IC[50] values are written in parentheses. The dialkoxy pharmacophores are colored in red.

Figure 4.
Fig. 4. The dimerization of wild type and mutant PDE4D catalytic domain. A: Purified wild type and R358D mutant protein were injected into a Superdex 200 (APbiotech) gel filtration column. Elution volumes for molecular weight standards are indicated. B: Glutaraldehyde-mediated cross-linking of the purified wild type and mutant proteins was performed as published [26]. The cross-linked proteins were separated by SDS–PAGE and stained with Coomassie brilliant blue R-250. Glutaraldehyde concentrations used for each lanes are, 1, 6, 11: 0%; 2, 7, 12: 0.01%; 3, 8, 13: 0.03%; 4, 9, 14: 0.1%; 5, 10, 15: 0.3%. Mutant catalytic domains of PDE4D were cloned into the pAcHLTA vector (BD Pharmingen) and expressed using a baculovirus expression system. Mutant proteins could not be overexpressed in Escherichia coli. They run in as slightly higher molecular weight due to hexa-histidine tags. In control experiments with wild type protein expressed in insect cells, the histidine tag did not affect cross-linking results (data not shown).

The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2002, 530, 53-58) copyright 2002.

Figures were selected by an automated process.