PDBsum entry 4x0f

Hydrolase/hydrolase inhibitor

PDB id: 4x0f

Contents

Protein chains

411 a.a.

Ligands

ROL ×2

Metals

_MG ×2

_ZN ×3

IOD ×2

PDB id:

4x0f

Name:

Hydrolase/hydrolase inhibitor

Title:

Crystal structure of crosslink stabilized long-form pde4b in complex with (r)-(-)-rolipram

Structure:

Camp-specific 3',5'-cyclic phosphodiesterase 4b. Chain: a, b. Fragment: unp residues 122-736. Synonym: dpde4,pde32. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pde4b, dpde4. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf21

Resolution:

3.22Å R-factor: 0.182 R-free: 0.222

Authors:

P.Cedervall,J.Pandit

Key ref:

P.Cedervall et al. (2015). Engineered stabilization and structural analysis of the autoinhibited conformation of PDE4. Proc Natl Acad Sci U S A, 112, E1414. PubMed id: 25775568 DOI: 10.1073/pnas.1419906112

Date:

21-Nov-14 Release date: 11-Mar-15

Protein chains

Q07343  (PDE4B_HUMAN) -  3',5'-cyclic-AMP phosphodiesterase 4B from Homo sapiens

Seq: 736 a.a.

Struc: 411 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.4.53 - 3',5'-cyclic-AMP phosphodiesterase.
• Reaction: 3',5'-cyclic AMP + H2O = AMP + H⁺

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

Added reference

DOI no: 10.1073/pnas.1419906112

Proc Natl Acad Sci U S A 112:E1414 (2015)

PubMed id: 25775568

Engineered stabilization and structural analysis of the autoinhibited conformation of PDE4.

P.Cedervall, A.Aulabaugh, K.F.Geoghegan, T.J.McLellan, J.Pandit.

ABSTRACT

Phosphodiesterase 4 (PDE4) is an essential contributor to intracellular signaling and an important drug target. The four members of this enzyme family (PDE4A to -D) are functional dimers in which each subunit contains two upstream conserved regions (UCR), UCR1 and -2, which precede the C-terminal catalytic domain. Alternative promoters, transcriptional start sites, and mRNA splicing lead to the existence of over 25 variants of PDE4, broadly classified as long, short, and supershort forms. We report the X-ray crystal structure of long form PDE4B containing UCR1, UCR2, and the catalytic domain, crystallized as a dimer in which a disulfide bond cross-links cysteines engineered into UCR2 and the catalytic domain. Biochemical and mass spectrometric analyses showed that the UCR2-catalytic domain interaction occurs in trans, and established that this interaction regulates the catalytic activity of PDE4. By elucidating the key structural determinants of dimerization, we show that only long forms of PDE4 can be regulated by this mechanism. The results also provide a structural basis for the long-standing observation of high- and low-affinity binding sites for the prototypic inhibitor rolipram.