PDBsum entry: 2zmf

Hydrolase

PDB id: 2zmf

Contents

Protein chains

177 a.a. *

Ligands

CMP ×2

Waters ×168

* Residue conservation analysis

PDB id:

2zmf

Name:

Hydrolase

Title:

Crystal structure of thE C-terminal gaf domain of human phosphodiesterase 10a

Structure:

Camp and camp-inhibited cgmp 3',5'-cyclic phospho 10a. Chain: a, b. Fragment: c-terminal gaf domain. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pde10a. Expressed in: cell free (escherichia coli).

Resolution:

2.10Å R-factor: 0.200 R-free: 0.225

Authors:

N.Handa,S.Kishishita,E.Mizohata,K.Omori,J.Kotera,T.Terada,M. S.Yokoyama,Riken Structural Genomics/proteomics Initiative

Key ref:

N.Handa et al. (2008). Crystal structure of the GAF-B domain from human phosphodiesterase 10A complexed with its ligand, cAMP. J Biol Chem, 283, 19657-19664. PubMed id: 18477562 DOI: 10.1074/jbc.M800595200

Date:

17-Apr-08 Release date: 29-Apr-08

Supersedes:

2e4s

Protein chains

Q9Y233  (PDE10_HUMAN) -  cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A

Seq: 779 a.a.

Struc: 177 a.a.

Enzyme reactions

• Enzyme class 1: 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 = CMP) matches with 52.17% similarity) + H(2)O = nucleoside 5'-phosphate

• Enzyme class 2: E.C.3.1.4.35 - 3',5'-cyclic-GMP phosphodiesterase.
• Reaction: Guanosine 3',5'-cyclic phosphate + H₂O = guanosine 5'-phosphate

Guanosine 3',5'-cyclic phosphate (Bound ligand (Het Group name = CMP) matches with 95.65% similarity) + H(2)O = guanosine 5'-phosphate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

 Gene Ontology (GO) functional annotation 

• Biochemical function: protein binding (1 term)

reference

DOI no: 10.1074/jbc.M800595200

J Biol Chem 283:19657-19664 (2008)

PubMed id: 18477562

Crystal structure of the GAF-B domain from human phosphodiesterase 10A complexed with its ligand, cAMP.

N.Handa, E.Mizohata, S.Kishishita, M.Toyama, S.Morita, T.Uchikubo-Kamo, R.Akasaka, K.Omori, J.Kotera, T.Terada, M.Shirouzu, S.Yokoyama.

ABSTRACT

Cyclic nucleotide phosphodiesterases (PDEs) catalyze the degradation of the cyclic nucleotides cAMP and cGMP, which are important second messengers. Five of the 11 mammalian PDE families have tandem GAF domains at their N termini. PDE10A may be the only mammalian PDE for which cAMP is the GAF domain ligand, and it may be allosterically stimulated by cAMP. PDE10A is highly expressed in striatal medium spiny neurons. Here we report the crystal structure of the C-terminal GAF domain (GAF-B) of human PDE10A complexed with cAMP at 2.1-angstroms resolution. The conformation of the PDE10A GAF-B domain monomer closely resembles those of the GAF domains of PDE2A and the cyanobacterium Anabaena cyaB2 adenylyl cyclase, except for the helical bundle consisting of alpha1, alpha2, and alpha5. The PDE10A GAF-B domain forms a dimer in the crystal and in solution. The dimerization is mainly mediated by hydrophobic interactions between the helical bundles in a parallel arrangement, with a large buried surface area. In the PDE10A GAF-B domain, cAMP tightly binds to a cNMP-binding pocket. The residues in the alpha3 and alpha4 helices, the beta6 strand, the loop between 3(10) and alpha4, and the loop between alpha4 and beta5 are involved in the recognition of the phosphate and ribose moieties. This recognition mode is similar to those of the GAF domains of PDE2A and cyaB2. In contrast, the adenine base is specifically recognized by the PDE10A GAF-B domain in a unique manner, through residues in the beta1 and beta2 strands.

Selected figure(s)

Figure 3.
FIGURE 3. Recognition of cAMP by the GAF-B domain of PDE10A. A, a semi-transparent surface representation, viewed from the opening of the cAMP-binding pocket. The bound cAMP molecule is represented by a yellow ball-and-stick model, with oxygen, nitrogen, and phosphorus atoms shown in red, blue, and purple, respectively. A simulated annealing omit [calc](|F[o]| - |F[c]|) map was calculated without the cAMP molecule atoms to 2.1-Å resolution, and was contoured at 3.0 . B, stereo diagram showing the cAMP recognition. The bound cAMP (yellow) and the interacting residues (white) are shown by ball-and-stick models, with oxygen, nitrogen, phosphorus, and sulfur atoms shown in red, blue, purple, and orange, respectively. Two water molecules are shown as red spheres. In the ribbon model, the β strands are cyan, the helices are salmon, the 3[10] helix is green, and the random coils are gray. Hydrogen bonds between cAMP and the protein are indicated by broken red lines.

Figure 4.
FIGURE 4. cNMP recognition by GAF domains. Hydrogen bonds are indicated by broken red lines. A, stereo diagram showing the superposition of GAF domains complexed with cNMP from PDE10A, PDE2A, and cyaB2. The GAF domains except for the helical bundles are represented by gray tube models. The cNMP molecules are represented by blue stick models. Amino acid side chains at positions equivalent to Phe^304 (PDE2A, Phe^438; cyaB2, Ile^308), Val^356 (PDE2A, Val^484; cyaB2, Ile^355), Asp^357 (PDE2A, Asp^485; cyaB2, Asp^356), Thr^360 (PDE2A, Thr^488; cyaB2, Thr^172/Asn^359), Thr^364 (PDE2A, Thr^492; cyaB2, Thr^176/Thr^363), Gln^383 (PDE2A, Glu^512; cyaB2, Gln^196/Gln^383), Val^385 (PDE2A, Val^514; cyaB2, Leu^198/Val^385), in PDE10A are shown, and backbone atoms at positions equivalent to Ile^330 (PDE2A, Ile^458; cyaB2, Ile^139/Phe^326) and Ala^331 (PDE2A, Ala^459; cyaB2, Ala^140/Ala^327) are shown. Residues making hydrophobic interactions with cNMP are orange, residues making hydrogen bonds to the O2' are sky blue, residues making water-mediated hydrogen bonds to bases are pink, and residues making hydrogen bonds to phosphate groups are green. One water molecule is shown, as a red sphere. B, stereo diagram showing the superimposed ball-and-stick models of the bases and the residues making direct hydrogen bonds to the bases. Residues in the PDE10A GAF-B domain complexed with cAMP are green, residues in the PDE2A GAF-B domain complexed with cGMP are magenta, residues in the cyaB2 GAF-A domain complexed with cAMP are yellow, and residues in the cyaB2 GAF-B domain complexed with cAMP are orange. Oxygen, nitrogen, and sulfur atoms are red, blue, and orange, respectively.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 19657-19664) copyright 2008.

Figures were selected by an automated process.