6TC7 | pdb_00006tc7

PAS-GAF bidomain of Glycine max phytochromeA

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth BBB]	KWL1	e6tc7BBB1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: KWL1	ECOD (develop294)
A [auth AAA]	KWL1	e6tc7AAA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: KWL1	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth AAA], B [auth BBB]	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
A [auth AAA], B [auth BBB]	PF08446	PAS fold (PAS_2)	PAS fold	The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth AAA], B [auth BBB]	Phytochrome	molecular sensor activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, nitrogenous group as acceptor phosphotransferase activity, alcohol group as acceptor protein histidine kinase activity transferase activity, transferring phosphorus-containing groups phosphorelay sensor kinase activity molecular function regulator activity catalytic activity identical protein binding protein binding molecular sensor activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, nitrogenous group as acceptor phosphotransferase activity, alcohol group as acceptor protein histidine kinase activity transferase activity, transferring phosphorus-containing groups phosphorelay sensor kinase activity molecular function regulator activity catalytic activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity molecular transducer activity photoreceptor activity signaling receptor activity	cellular response to stimulus response to light stimulus cellular response to red or far red light regulation of cellular process response to stimulus signaling response to red or far red light detection of abiotic stimulus cell communication cellular response to environmental stimulus cellular response to light stimulus signal transduction phototransduction detection of light stimulus cellular response to stimulus response to light stimulus cellular response to red or far red light regulation of cellular process response to stimulus signaling response to red or far red light detection of abiotic stimulus cell communication cellular response to environmental stimulus cellular response to light stimulus signal transduction phototransduction detection of light stimulus detection of external stimulus regulation of biological process red or far-red light signaling pathway biological regulation response to external stimulus cellular response to radiation detection of stimulus red, far-red light phototransduction cellular process response to radiation response to abiotic stimulus cellular response to abiotic stimulus protein-tetrapyrrole linkage primary metabolic process gene expression macromolecule biosynthetic process protein-bilin linkage protein maturation biosynthetic process protein-phycocyanobilin linkage metabolic process protein metabolic process macromolecule metabolic process detection of visible light RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth AAA], B [auth BBB]	IPR012129	Phytochrome A/B/C/D/E	Family
A [auth AAA], B [auth BBB]	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A [auth AAA], B [auth BBB]	IPR003661	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain	Domain
A [auth AAA], B [auth BBB]	IPR013654	PAS fold-2	Domain
A [auth AAA], B [auth BBB]	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
A [auth AAA], B [auth BBB]	IPR000700	PAS-associated, C-terminal	Domain
A [auth AAA], B [auth BBB]	IPR013516	Phytochrome chromophore binding site	Binding Site
A [auth AAA], B [auth BBB]	IPR003018	GAF domain	Domain
A [auth AAA], B [auth BBB]	IPR001294	Phytochrome	Family
A [auth AAA], B [auth BBB]	IPR016132	Phytochrome chromophore attachment domain	Domain
A [auth AAA], B [auth BBB]	IPR013767	PAS fold	Domain
A [auth AAA], B [auth BBB]	IPR013515	Phytochrome, central region	Domain
A [auth AAA], B [auth BBB]	IPR000014	PAS domain	Domain
A [auth AAA], B [auth BBB]	IPR043150	Phytochrome, PHY domain superfamily	Homologous Superfamily
A [auth AAA], B [auth BBB]	IPR035965	PAS domain superfamily	Homologous Superfamily
A [auth AAA], B [auth BBB]	IPR005467	Histidine kinase domain	Domain
A [auth AAA], B [auth BBB]	IPR029016	GAF-like domain superfamily	Homologous Superfamily

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.