1F5M

STRUCTURE OF THE GAF DOMAIN

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1f5ma_	Alpha and beta proteins (a+b)	Profilin-like	GAF domain-like	GAF domain	Hypothetical protein ykl069wp	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1f5mb_	Alpha and beta proteins (a+b)	Profilin-like	GAF domain-like	GAF domain	Hypothetical protein ykl069wp	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	GAF domain	8023738	4001852	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GAF domain-like	8036118	3000080	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	GAF domain-like	8036118	3000080	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	GAF	e1f5mA1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: GAF	ECOD (1.6)
B	GAF	e1f5mB1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: GAF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.450.40	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	GAF domain	CATH (4.3.0)
B	3.30.450.40	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	GAF domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01590	GAF domain (GAF)	GAF domain	This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regul ...	This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalysed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and 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. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	GAF	oxidoreductase activity, acting on a sulfur group of donors oxidoreductase activity oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor L-methionine-(R)-S-oxide reductase activity catalytic activity	cellular response to stimulus response to oxidative stress cellular response to chemical stimulus response to stimulus cellular response to stress response to stress response to chemical cellular response to oxidative stress cellular process cellular response to chemical stress	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR003018	GAF domain	Domain
A, B	IPR029016	GAF-like domain superfamily	Homologous Superfamily
A, B	IPR000614	Free Met sulfoxide reductase conserved site	Conserved Site
A, B	IPR051330	Phosphatase regulators and Met sulfoxide reductases	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.