Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.61 kDa 
• Atom Count: 3000 
• Modelled Residue Count: 349 
• Deposited Residue Count: 378 
• Unique protein chains: 1

2ZMF

Crystal structure of the C-terminal GAF domain of human phosphodiesterase 10A

• DOI: 10.2210/pdb2ZMF/pdb
• Entry: 2ZMF supersedes: 2E4S

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2008-04-17 Released: 2008-04-29 
• Deposition Author(s): Handa, N., Kishishita, S., Mizohata, E., Omori, K., Kotera, J., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.225 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 

Literature

Crystal Structure of the GAF-B Domain from Human Phosphodiesterase 10A Complexed with Its Ligand, cAMP

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

(2008) J Biol Chem 283: 19657-19664

• PubMed: 18477562 
• DOI: 10.1074/jbc.M800595200
• Primary Citation of Related Structures:  
  2ZMF


• PubMed 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.

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Organizational Affiliation: 

Systems and Structural Biology Center, Yokohama Institute, RIKEN, Yokohama 230-0045, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A	A, B	189	Homo sapiens	Mutation(s): 0  Gene Names: PDE10A EC: 3.1.4.17 (PDB Primary Data), 3.1.4.35 (UniProt)
Find proteins for Q9Y233 (Homo sapiens) Explore Q9Y233  Go to UniProtKB:  Q9Y233
NIH Common Fund Data Resources
PHAROS:  Q9Y233 GTEx:  ENSG00000112541

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMP	C [auth A], D [auth B]	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE C10 H12 N5 O6 P IVOMOUWHDPKRLL-KQYNXXCUSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.225 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.506	α = 90
b = 74.506	β = 90
c = 146.524	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-04-17 
• Released Date: 2008-04-29 
Deposition Author(s): Handa, N., Kishishita, S., Mizohata, E., Omori, K., Kotera, J., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
• This entry supersedes: 2E4S

Revision History  

• Version 1.0: 2008-04-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance