PDBsum entry 3ibj

Hydrolase

PDB id: 3ibj

Contents

Protein chain

661 a.a. *

Metals

_MG ×2

_ZN ×2

Waters ×191

* Residue conservation analysis

PDB id:

3ibj

Name:

Hydrolase

Title:

X-ray structure of pde2a

Structure:

Cgmp-dependent 3',5'-cyclic phosphodiesterase. Chain: a, b. Fragment: unp residues 215-900. Synonym: cyclic gmp-stimulated phosphodiesterase, cgs-pde, cgspde. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pde2a. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.

Resolution:

3.02Å R-factor: 0.215 R-free: 0.311

Authors:

J.Pandit

Key ref:

J.Pandit et al. (2009). Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct. Proc Natl Acad Sci U S A, 106, 18225-18230. PubMed id: 19828435 DOI: 10.1073/pnas.0907635106

Date:

16-Jul-09 Release date: 27-Oct-09

Protein chains

O00408  (PDE2A_HUMAN) -  cGMP-dependent 3',5'-cyclic phosphodiesterase from Homo sapiens

Seq: 941 a.a.

Struc: 661 a.a.

Enzyme reactions

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

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

Added reference

DOI no: 10.1073/pnas.0907635106

Proc Natl Acad Sci U S A 106:18225-18230 (2009)

PubMed id: 19828435

Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct.

J.Pandit, M.D.Forman, K.F.Fennell, K.S.Dillman, F.S.Menniti.

ABSTRACT

We report the X-ray crystal structure of a phosphodiesterase (PDE) that includes both catalytic and regulatory domains. PDE2A (215-900) crystallized as a dimer in which each subunit had an extended organization of regulatory GAF-A and GAF-B and catalytic domains connected by long alpha-helices. The subunits cross at the GAF-B/catalytic domain linker, and each side of the dimer contains in series the GAF-A and GAF-B of one subunit and the catalytic domain of the other subunit. A dimer interface extends over the entire length of the molecule. The substrate binding pocket of each catalytic domain is occluded by the H-loop. We deduced from comparisons with structures of isolated, ligand-bound catalytic subunits that the H-loop swings out to allow substrate access. However, in dimeric PDE2A (215-900), the H-loops of the two catalytic subunits pack against each other at the dimer interface, necessitating movement of the catalytic subunits to allow for H-loop movement. Comparison of the unliganded GAF-B of PDE2A (215-900) with previous structures of isolated, cGMP-bound GAF domains indicates that cGMP binding induces a significant shift in the GAF-B/catalytic domain linker. We propose that cGMP binding to GAF-B causes movement, through this linker region, of the catalytic domains, such that the H-loops no longer pack at the dimer interface and are, instead, free to swing out to allow substrate access. This increase in substrate access is proposed as the basis for PDE2A activation by cGMP and may be a general mechanism for regulation of all PDEs.

Selected figure(s)

Figure 1.
Structure of hPDE2A (215–900). The asymmetric unit contains two molecules, A and B, related by a noncrystallographic 2-fold axis of symmetry, which, in this view, is roughly parallel to the plane of the paper in the vertical direction. The three domains are labeled in the figure, as well as the linker helices LH1 and LH2 that connect them. Molecule B is shown in surface representation, and molecule A is shown in a ribbons representation, with the ribbons colored by crystallographic B-factor, blue being low and red being high. Regions of the structure with higher B-factors, such as the linker between the GAF-B domain and the catalytic domain, are expected to be more flexible. All side chains from molecule A that are within 3.5 Å of molecule B are shown as magenta sticks, The dimer interface extends over the surface of the entire molecule. The two catalytic sites in the vicinity of the Zn^2+ and Mg^2+ ions (shown as gray and green spheres) mutually occlude each other at the dimer interface. All figures showing the structure were generated with PyMOL (www.pymol.org).

Figure 3.
The two catalytic sites mutually occlude each other at the dimer interface. (A) The catalytic domain of a single subunit of the PDE2A (215–900) dimer is shown in ribbons representation, with the H-loop colored in magenta and the M-loop colored in blue. The active site, whose location can be inferred from the position of the Zn^2+ and Mg^2+ ions (shown as gray and green spheres) is partially occupied by residues from the H-loop. Residues 840–850 of the M-loop have not been modeled due to disorder and are indicated by a dotted line. (B) The second subunit is shown as a semitransparent gray surface, as well as in ribbons representation, keeping exactly the same orientation as in panel A. The H-loop is blocked from swinging out of the active site by the dimer interface.

Figures were selected by an automated process.