4E04 | pdb_00004e04

RpBphP2 chromophore-binding domain crystallized by homologue-directed mutagenesis.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
B	d4e04b2	Alpha and beta proteins (a+b)	Profilin-like	GAF domain-like	automated matches	automated matches	(Rhodopseudomonas palustris CGA009 ) [TaxId: 258594 ],	SCOPe (2.08)
B	d4e04b1	Alpha and beta proteins (a+b)	Profilin-like	PYP-like sensor domain (PAS domain)	automated matches	automated matches	(Rhodopseudomonas palustris CGA009 ) [TaxId: 258594 ],	SCOPe (2.08)
B	d4e04b3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Rhodopseudomonas palustris CGA009 ) [TaxId: 258594 ],	SCOPe (2.08)
A	d4e04a2	Alpha and beta proteins (a+b)	Profilin-like	GAF domain-like	automated matches	automated matches	(Rhodopseudomonas palustris CGA009 ) [TaxId: 258594 ],	SCOPe (2.08)
A	d4e04a1	Alpha and beta proteins (a+b)	Profilin-like	PYP-like sensor domain (PAS domain)	automated matches	automated matches	(Rhodopseudomonas palustris CGA009 ) [TaxId: 258594 ],	SCOPe (2.08)
A	d4e04a3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Rhodopseudomonas palustris CGA009 ) [TaxId: 258594 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e4e04B3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (v294.1)
A	EF-hand_1,S_100	e4e04A1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: SH3	T: SH3	F: EF-hand_1,S_100	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

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	Bacteriophytochrome (Light-regulated signal transduction histidine kinase), PhyB1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding 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 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 catalytic activity molecular transducer activity photoreceptor activity signaling receptor activity phosphorelay response regulator activity cation binding metal ion binding	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 osmosensory signaling via phosphorelay pathway response to stimulus signaling cellular response to chemical stress intracellular signal transduction cellular response to environmental stimulus cell communication osmosensory signaling pathway cellular response to stress response to stress signal transduction response to osmotic stress phosphorelay signal transduction system cellular response to osmotic stress cellular response to chemical stimulus response to chemical response to abiotic stimulus cellular response to abiotic stimulus detection of light stimulus response to light stimulus detection of external stimulus detection of stimulus detection of visible light response to external 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	IPR004358	Signal transduction histidine kinase-related protein, C-terminal	Domain
A, B	IPR036097	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily	Homologous Superfamily
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	IPR050351	Bacteriophytochrome/Sensor protein kinase WalK/GraS-like	Family
A, B	IPR003018	GAF domain	Domain
A, B	IPR029016	GAF-like domain superfamily	Homologous Superfamily
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.