6R27

Crystallographic superstructure of the photosensory core module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) locked in a Pr-like state

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)
A	PAS_2	e6r27A3	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_2	ECOD (1.6)
A	PHY	e6r27A1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PHY	ECOD (1.6)
A	GAF	e6r27A2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: GAF	ECOD (1.6)
B	PAS_2	e6r27B1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_2	ECOD (1.6)
B	PHY	e6r27B2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PHY	ECOD (1.6)
B	GAF	e6r27B3	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: GAF	ECOD (1.6)
C	PAS_2	e6r27C1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_2	ECOD (1.6)
C	PHY	e6r27C3	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PHY	ECOD (1.6)
C	GAF	e6r27C2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: GAF	ECOD (1.6)
D	PAS_2	e6r27D2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_2	ECOD (1.6)
D	PHY	e6r27D1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PHY	ECOD (1.6)
D	GAF	e6r27D3	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: GAF	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, B, C, D	PF00360	Phytochrome region (PHY)	Phytochrome region	Phytochromes are red/far-red photochromic biliprotein photoreceptors which regulate plant development. They are widely represented in both photosynthetic and non-photosynthetic bacteria and are known in a variety of fungi. Although sequence similarit ...	Phytochromes are red/far-red photochromic biliprotein photoreceptors which regulate plant development. They are widely represented in both photosynthetic and non-photosynthetic bacteria and are known in a variety of fungi. Although sequence similarities are low, this domain is structurally related to Pfam:PF01590 [1], which is generally located immediately N-terminal to this domain. Compared with Pfam:PF01590, this domain carries an additional tongue-like hairpin loop between the fifth beta-sheet and the sixth alpha-helix which functions to seal the chromophore pocket and stabilise the photoactivated far-red-absorbing state (Pfr) [1]. The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue [1].	Domain
A, B, C, D	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, B, C, D	Bacteriophytochrome protein	enzyme regulator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, nitrogenous group as acceptor enzyme regulator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, nitrogenous group as acceptor phosphotransferase activity, alcohol group as acceptor protein histidine kinase activity transferase activity, transferring phosphorus-containing groups molecular sensor activity phosphorelay sensor kinase activity molecular transducer activity phosphorelay response regulator activity cation binding ion binding binding metal ion binding small molecule binding red or far-red light photoreceptor activity photoreceptor activity signaling receptor activity	regulation of cellular process 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 biological process biological regulation primary metabolic process regulation of cellular process 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 biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cellular response to stimulus response to light stimulus cellular response to red or far red light 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 red or far-red light signaling pathway response to external stimulus cellular response to radiation detection of stimulus red, far-red light phototransduction response to radiation response to abiotic stimulus cellular response to abiotic stimulus osmosensory signaling via phosphorelay pathway cellular response to chemical stress intracellular signal transduction osmosensory signaling pathway cellular response to stress response to stress response to osmotic stress phosphorelay signal transduction system cellular response to osmotic stress cellular response to chemical stimulus response to chemical detection of visible light	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR013515	Phytochrome, central region	Domain
A, B, C, D	IPR036097	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily	Homologous Superfamily
A, B, C, D	IPR043150	Phytochrome, PHY domain superfamily	Homologous Superfamily
A, B, C, D	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A, B, C, D	IPR003661	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain	Domain
A, B, C, D	IPR013654	PAS fold-2	Domain
A, B, C, D	IPR035965	PAS domain superfamily	Homologous Superfamily
A, B, C, D	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
A, B, C, D	IPR005467	Histidine kinase domain	Domain
A, B, C, D	IPR003018	GAF domain	Domain
A, B, C, D	IPR029016	GAF-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR052545	Light-responsive regulatory protein	Family
A, B, C, D	IPR001294	Phytochrome	Family
A, B, C, D	IPR016132	Phytochrome chromophore attachment domain	Domain

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.