5LLY

Photosensory Module of Bacteriophytochrome linked Diguanylyl Cyclase from Idiomarina species A28L

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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 [auth D]	PAS_2	e5llyD1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_2	ECOD (1.6)
A [auth D]	PHY	e5llyD3	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PHY	ECOD (1.6)
A [auth D]	GAF	e5llyD2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: GAF	ECOD (1.6)
B [auth A]	PAS_2	e5llyA3	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_2	ECOD (1.6)
B [auth A]	PHY	e5llyA2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PHY	ECOD (1.6)
B [auth A]	GAF	e5llyA1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: GAF	ECOD (1.6)
C	PAS_2	e5llyC1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_2	ECOD (1.6)
C	PHY	e5llyC2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PHY	ECOD (1.6)
C	GAF	e5llyC3	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: GAF	ECOD (1.6)
D [auth B]	PAS_2	e5llyB2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_2	ECOD (1.6)
D [auth B]	PHY	e5llyB3	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PHY	ECOD (1.6)
D [auth B]	GAF	e5llyB1	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)
B [auth A]	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 [auth D], B [auth A], C, D [auth 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
A [auth D], B [auth A], C, D [auth B]	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 [auth D], B [auth A], C, D [auth B]	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 D], B [auth A], C, D [auth B]	Diguanylate cyclase (GGDEF) domain-containing protein	molecular transducer activity photoreceptor activity signaling receptor activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding molecular transducer activity photoreceptor activity signaling receptor activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding metal ion binding	regulation of cellular process cellular biosynthetic 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process detection of light stimulus response to light stimulus detection of external stimulus detection of stimulus response to stimulus detection of visible light response to external stimulus response to abiotic stimulus response to radiation detection of abiotic stimulus	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], B [auth A], C, D [auth B]	IPR013515	Phytochrome, central region	Domain
A [auth D], B [auth A], C, D [auth B]	IPR000160	GGDEF domain	Domain
A [auth D], B [auth A], C, D [auth B]	IPR043150	Phytochrome, PHY domain superfamily	Homologous Superfamily
A [auth D], B [auth A], C, D [auth B]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A [auth D], B [auth A], C, D [auth B]	IPR013654	PAS fold-2	Domain
A [auth D], B [auth A], C, D [auth B]	IPR035965	PAS domain superfamily	Homologous Superfamily
A [auth D], B [auth A], C, D [auth B]	IPR003018	GAF domain	Domain
A [auth D], B [auth A], C, D [auth B]	IPR029016	GAF-like domain superfamily	Homologous Superfamily
A [auth D], B [auth A], C, D [auth B]	IPR001294	Phytochrome	Family
A [auth D], B [auth A], C, D [auth B]	IPR029787	Nucleotide cyclase	Homologous Superfamily
A [auth D], B [auth A], C, D [auth B]	IPR016132	Phytochrome chromophore attachment domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.