2OOL

Crystal structure of the chromophore-binding domain of an unusual bacteriophytochrome RpBphP3 from R. palustris

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	d2oola1	Alpha and beta proteins (a+b)	Profilin-like	GAF domain-like	GAF domain	Sensor protein PhyB2	(Rhodopseudomonas palustris CGA009 ) [TaxId: 258594 ],	SCOPe (2.08)
A	d2oola2	Alpha and beta proteins (a+b)	Profilin-like	PYP-like sensor domain (PAS domain)	BphP N-terminal domain-like	Sensor protein PhyB2	(Rhodopseudomonas palustris CGA009 ) [TaxId: 258594 ],	SCOPe (2.08)
B	d2oolb1	Alpha and beta proteins (a+b)	Profilin-like	GAF domain-like	GAF domain	Sensor protein PhyB2	(Rhodopseudomonas palustris CGA009 ) [TaxId: 258594 ],	SCOPe (2.08)
B	d2oolb2	Alpha and beta proteins (a+b)	Profilin-like	PYP-like sensor domain (PAS domain)	BphP N-terminal domain-like	Sensor protein PhyB2	(Rhodopseudomonas palustris CGA009 ) [TaxId: 258594 ],	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	8022818	4001852	SCOP2 (2022-06-29)
A	SCOP2 Family	BphP N-terminal domain-like	8022820	4002319	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GAF domain-like	8035198	3000080	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PYP-like sensor domain (PAS domain)	8035200	3000471	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	PYP-like sensor domain (PAS domain)	8035200	3000471	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GAF domain-like	8035198	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	PAS_2	e2oolA2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_2	ECOD (1.6)
A	GAF	e2oolA1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: GAF	ECOD (1.6)
B	PAS_2	e2oolB2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_2	ECOD (1.6)
B	GAF	e2oolB1	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	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)
A	3.30.450.40	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	GAF domain	CATH (4.3.0)
B	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS 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
A, 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, B	Sensor protein	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule 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 molecular transducer activity photoreceptor activity signaling receptor activity identical protein binding protein 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic 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 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 regulation of gene expression 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, B	IPR013515	Phytochrome, central region	Domain
A, B	IPR036097	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily	Homologous Superfamily
A, B	IPR052162	Two-component sensor kinase/Photoreceptor	Family
A, B	IPR043150	Phytochrome, PHY domain superfamily	Homologous Superfamily
A, B	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A, B	IPR003661	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain	Domain
A, B	IPR013654	PAS fold-2	Domain
A, B	IPR035965	PAS domain superfamily	Homologous Superfamily
A, B	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
A, B	IPR005467	Histidine kinase domain	Domain
A, B	IPR003018	GAF domain	Domain
A, B	IPR029016	GAF-like domain superfamily	Homologous Superfamily
A, B	IPR001294	Phytochrome	Family
A, B	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.