PDBsum entry: 1mc0

Hydrolase

PDB id: 1mc0

Contents

Protein chain

341 a.a. *

Ligands

PCG

Waters ×38

* Residue conservation analysis

PDB id:

1mc0

Name:

Hydrolase

Title:

Regulatory segment of mouse 3',5'-cyclic nucleotide phosphod 2a, containing the gaf a and gaf b domains

Structure:

3',5'-cyclic nucleotide phosphodiesterase 2a. Chain: a. Fragment: regulatory domain (residues 207-566). Engineered: yes. Mutation: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: pde2a. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.86Å R-factor: 0.221 R-free: 0.266

Authors:

S.Martinez,A.Wu,N.Glavas,X.Tang,S.Turley,W.Hol,J.Beavo

Key ref:

S.E.Martinez et al. (2002). The two GAF domains in phosphodiesterase 2A have distinct roles in dimerization and in cGMP binding. Proc Natl Acad Sci U S A, 99, 13260-13265. PubMed id: 12271124 DOI: 10.1073/pnas.192374899

Date:

04-Aug-02 Release date: 02-Oct-02

Protein chain

Q922S4  (PDE2A_MOUSE) -  cGMP-dependent 3',5'-cyclic phosphodiesterase

Seq: 916 a.a.

Struc: 341 a.a.

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

Nucleoside 3',5'-cyclic phosphate (Bound ligand (Het Group name = PCG) matches with 50.00% similarity) + H(2)O = nucleoside 5'-phosphate

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

 Gene Ontology (GO) functional annotation 

• Biochemical function: protein binding (1 term)

Added reference

DOI no: 10.1073/pnas.192374899

Proc Natl Acad Sci U S A 99:13260-13265 (2002)

PubMed id: 12271124

The two GAF domains in phosphodiesterase 2A have distinct roles in dimerization and in cGMP binding.

S.E.Martinez, A.Y.Wu, N.A.Glavas, X.B.Tang, S.Turley, W.G.Hol, J.A.Beavo.

ABSTRACT

Cyclic nucleotide phosphodiesterases (PDEs) regulate all pathways that use cGMP or cAMP as a second messenger. Five of the 11 PDE families have regulatory segments containing GAF domains, 3 of which are known to bind cGMP. In PDE2 binding of cGMP to the GAF domain causes an activation of the catalytic activity by a mechanism that apparently is shared even in the adenylyl cyclase of Anabaena, an organism separated from mouse by 2 billion years of evolution. The 2.9-A crystal structure of the mouse PDE2A regulatory segment reported in this paper reveals that the GAF A domain functions as a dimerization locus. The GAF B domain shows a deeply buried cGMP displaying a new cGMP-binding motif and is the first atomic structure of a physiological cGMP receptor with bound cGMP. Moreover, this cGMP site is located well away from the region predicted by previous mutagenesis and structural genomic approaches.

Selected figure(s)

Figure 1.
Fig. 1. (a) Two views of the structure of the regulatory segment of mouse PDE2A. Each PDE2A subunit contains a GAF A and a GAF B domain. The GAF A domain and seven turns of the connecting helices form a dimer interface. The two GAF B domains are far apart and contain the cGMP-binding sites. (Upper) View showing the dimer interface of the regulatory segment. (Lower) View 70° rotated with respect to A showing the Y-shape and the disulfide at C386 most clearly. cGMP is shown in red. The overall dimensions of the regulatory segment dimer are 105 × 92 × 71 Å. (b and c) Stereo images comparing GAF B with GAF A or YKG9. The C positions of the 11 residues that contact cGMP are shown as red spheres. (b) PDE2A GAF B (blue, with bound cGMP) and PDE2A GAF A (green) is shown after least-squares superposition of C positions. There are significant main-chain differences in the GAF pocket. Note that the main chain from the N terminus of helix 4 in GAF A clashes with the guanine ring of cGMP in GAF B. (c) Superposition of the C positions of PDE2A GAF B onto YKG9. Note that the loop in GAF B that contacts the guanine ring through D438 and F439 is turned away in YKG9. Helix 4 in GAF B is another significant difference between GAF B and YKG9. The conserved NKFDE motif predicted in early studies to be involved in cGMP binding (29) is shown in gray in GAF B. The five conserved residues in this loop (N, K, F, D, and E) are indicated by black spheres. The first four residues from the YKG9 model (monomer A, residues 4-7) point away from the domain and have been deleted for clarity.

Figure 3.
Fig. 3. cGMP binding by PDE2A. (A) Electron density in a Sigma A-weighted omit map contoured at the 1.0 level shown together with cGMP bound to the GAF B domain of PDE2A. The density at the phosphate is 5 . Also shown is the critical Asp D439 that interacts with the guanine base with both its side-chain carboxylate and main-chain amino groups. This figure was prepared with BOBSCRIPT (31) and rendered with RASTER3D (32). (B) Close-up view of the cGMP-binding site in GAF B. Shown are six side chains that make hydrogen bonds to the cGMP, one that stacks with the guanine ring, and two that make backbone amide contacts. Helix 4 and strand 3' are depicted as coils for visibility of the cGMP. This figure was made with MOLSCRIPT (31) and RASTER3D (32). (C) Diagram showing all of the close interactions between cGMP and GAF B. The diagram was produced with LIGPLOT (33). The general features of cGMP binding in the GAF B structure are consistent with many of the predictions made from binding studies of PDE2 and PDE6 with cyclic nucleotide analogues. These studies suggested that cGMP would be bound in the anti-conformation, that contacts are made to C6, N1, and C2 amino group of the guanine ring and 2'O of the ribose ring, and that there are similar or identical types of contacts to the exocyclic oxygens (21, 26, 34). (D) cGMP and cAMP competition binding curves [against (3H)cGMP] for the wild-type regulatory segment of mouse PDE2A. A nitrocellulose filter-binding assay was used (18). Protein concentration was 0.6 nM.

Figures were selected by the author.