title: Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor.
abstract: GAF domains are ubiquitous motifs present in cyclic GMP (cGMP)-regulated cyclic nucleotide phosphodiesterases, certain adenylyl cyclases, the bacterial transcription factor FhlA, and hundreds of other signaling and sensory proteins from all three kingdoms of life. The crystal structure of the Saccharomyces cerevisiae YKG9 protein was determined at 1.9 A resolution. The structure revealed a fold that resembles the PAS domain, another ubiquitous signaling and sensory transducer. YKG9 does not bind cGMP, but the isolated first GAF domain of phosphodiesterase 5 binds with K:(d) = 650 nM. The cGMP binding site of the phosphodiesterase GAF domain was identified by homology modeling and site-directed mutagenesis, and consists of conserved Arg, Asn, Lys and Asp residues. The structural and binding studies taken together show that the cGMP binding GAF domains form a new class of cyclic nucleotide receptors distinct from the regulatory domains of cyclic nucleotide-regulated protein kinases and ion channels.
authors.affiliation: Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0580, USA.
authors.forename: Y S
authors.initials: YS
authors.lastname: Ho
authors.forename: L M
authors.initials: LM
authors.lastname: Burden
authors.forename: J H
authors.initials: JH
authors.lastname: Hurley
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry; D001665:Binding Sites; D002352:Carrier Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D003285:Contractile Proteins; D018360:Crystallography, X-Ray; D006152:Cyclic GMP / Q000378:metabolism; D054706:Cyclic Nucleotide Phosphodiesterases, Type 5; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D047908:Intracellular Signaling Peptides and Proteins; D008840:Microfilament Proteins / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D010727:Phosphoric Diester Hydrolases / Q000737:chemistry; D020283:Photoreceptors, Microbial; D051304:Profilins; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000737:chemistry* / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins; D016415:Sequence Alignment; D015398:Signal Transduction
chemical_list: D001426:Bacterial Proteins; D002352:Carrier Proteins; D003285:Contractile Proteins; D005656:Fungal Proteins; D047908:Intracellular Signaling Peptides and Proteins; D008840:Microfilament Proteins; D020283:Photoreceptors, Microbial; D051304:Profilins; D011994:Recombinant Proteins; D029701:Saccharomyces cerevisiae Proteins; C416042:YKL069W protein, S cerevisiae; C022994:cyclic GMP-binding protein; C050162:photoactive yellow protein, Bacteria; D010727:Phosphoric Diester Hydrolases; C521386:PDE5 protein, S cerevisiae; D054706:Cyclic Nucleotide Phosphodiesterases, Type 5; D006152:Cyclic GMP