GAF

Domain present in phytochromes and cGMP-specific phosphodiesterases.

• SMART accession number: SM00065
• Description: Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.
• Interpro abstract (IPR003018): This domain is present in phytochromes and cGMP-specific phosphodiesterases. cGMP-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17) catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. A phytochrome is a regulatory photoreceptor which exists in 2 forms that are reversibly interconvertible by light, the PR form that absorbs maximally in the red region of the spectrum, and the PFR form that absorbs maximally in the far-red region. This domain is also found in NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.

There are 7966 GAF domains in 6944 proteins in SMART's nrdb database.

Cellular role (predicted cellular role)

Binding / catalysis: chromophore-binding

Literature (relevant references for this domain)

Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

• Aravind L, Ponting CP
• The GAF domain: an evolutionary link between diverse phototransducing proteins.
• Trends Biochem Sci. 1997; 22: 458-9

• McAllister-Lucas LM et al.
• An essential aspartic acid at each of two allosteric cGMP-binding sites of a cGMP-specific phosphodiesterase.
• J Biol Chem. 1995; 270: 30671-9

The amino acid sequences of all known cGMP-binding phosphodiesterases (PDEs) contain internally homologous repeats (a and b) that are 80-90 residues in length and are arranged in tandem within the putative cGMP-binding domains. In the bovine lung cGMP-binding, cGMP-specific PDE (cGB-PDE or PDE5A), these repeats span residues 228-311 (a) and 410-500 (b). An aspartic acid (residue 289 or 478) that is invariant in repeats a and b of all known cGMP-binding PDEs was changed to alanine by site-directed mutagenesis of cGB-PDE, and wild type (WT) and mutant cGB-PDEs were expressed in COS-7 cells. Purified bovine lung cGB-PDE (native) and WT cGB-PDE displayed identical cGMP-binding kinetics, with approximately 1.8 microM cGMP required for half-maximal saturation. The D289A mutant showed decreased affinity for cGMP (Kd > 10 microM) and the D478A mutant showed increased affinity for cGMP (Kd approximately 0.5 microM) as compared to WT and native cGB-PDE. WT and native cGB-PDE displayed an identical curvilinear profile of cGMP dissociation which was consistent with the presence of distinct slowly dissociating (koff = 0.26 h-1) and rapidly dissociating (koff = 1.00 h-1) sites of cGMP binding. In contrast, the D289A mutant displayed a single koff = 1.24 h-1, which was similar to the calculated koff for the fast site of WT and native cGB-PDE, and the D478A mutant displayed a single koff = 0.29 h-1, which was similar to that calculated for the slow site of WT and native cGB-PDE. These results were consistent with the loss of a slow cGMP-binding site in repeat a of the D289A mutant cGB-PDE, and the loss of a fast site in repeat b of the D478A mutant, suggesting that cGB-PDE possesses two distinct cGMP-binding sites located at repeats a and b, with the invariant aspartic acid being crucial for interaction with cGMP at each site.

Disease (disease genes where sequence variants are found in this domain)

SwissProt sequences and OMIM curated human diseases associated with missense mutations within the GAF domain.

Protein	Disease
Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta precursor (SRS)(SMART)	OMIM:180072: Night blindness, congenital stationary, type 3 OMIM:163500: Retinitis pigmentosa, autosomal recessive
Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha (SRS)(SMART)	OMIM:180071: Retinitis pigmentosa, autosomal recessive

Metabolism (metabolic pathways involving proteins which contain this domain)

% proteins involved	KEGG pathway ID	Description
43.91	map02020	Two-component system - General
21.07	map02060	Phosphotransferase system (PTS)
11.17	map00230	Purine metabolism
9.39	map00910	Nitrogen metabolism
6.85	map04914	Progesterone-mediated oocyte maturation
1.78	map02030	Bacterial chemotaxis - General
1.78	map03090	Type II secretion system
0.51	map00562	Inositol phosphate metabolism
0.51	map00632	Benzoate degradation via CoA ligation
0.25	map00260	Glycine, serine and threonine metabolism
0.25	map00280	Valine, leucine and isoleucine degradation
0.25	map00760	Nicotinate and nicotinamide metabolism
0.25	map04510	Focal adhesion
0.25	map03320	PPAR signaling pathway
0.25	map00071	Fatty acid metabolism
0.25	map04810	Regulation of actin cytoskeleton
0.25	map00410	beta-Alanine metabolism
0.25	map04020	Calcium signaling pathway
0.25	map00640	Propanoate metabolism
0.25	map03060	Protein export
0.25	map00540	Lipopolysaccharide biosynthesis

This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with GAF domain which could be assigned to a KEGG orthologous group, and not all proteins containing GAF domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

Structure (3D structures containing this domain)

3D Structures of GAF domains in PDB

PDB code	Title
1f5m	Structure of the gaf domain
1mc0	Regulatory segment of mouse 3',5'-cyclic nucleotide phosphodiesterase 2a, containing the gaf a and gaf b domains
1vhm	Crystal structure of an hypothetical protein
1ykd	Crystal structure of the tandem gaf domains from a cyanobacterial adenylyl cyclase: novel modes of ligand- binding and dimerization
1ztu	Structure of the chromophore binding domain of bacterial phytochrome
2k2n
2k31	Solution structure of cgmp-binding gaf domain of phosphodiesterase 5
2kli
2koi
2o9b	Crystal structure of bacteriophytochrome chromophore binding domain
2o9c	Crystal structure of bacteriophytochrome chromophore binding domain at 1.45 angstrom resolution
2ool	Crystal structure of the chromophore-binding domain of an unusual bacteriophytochrome rpbphp3 from r. palustris
2qyb	Crystal structure of the gaf domain region of putative membrane protein from geobacter sulfurreducens pca
2vea
2vjw
2vks
2vzw
2w3d
2w3e
2w3f
2w3g
2w3h
2zmf	Crystal structure of the c-terminal gaf domain of human phosphodiesterase 10a
3bjc	Crystal structure of the pde5a catalytic domain in complex with a novel inhibitor
3c2w
3ci6	Crystal structure of the gaf domain from acinetobacter phosphoenolpyruvate-protein phosphotransferase
3cit	Crystal structure of the gaf domain of a putative sensor histidine kinase from pseudomonas syringae pv. tomato
3dba	Crystal structure of the cgmp-bound gaf a domain from the photoreceptor phosphodiesterase 6c
3e0y
3eea
3g6o
3hcy
3ibj
3ibr

Links (links to other resources describing this domain)

• INTERPRO: IPR003018