4RQ9 | pdb_00004rq9

Crystal structure of the chromophore-binding domain of Stigmatella aurantiaca bacteriophytochrome (Thr289His mutant) in the Pr state

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d4rq9a2	Alpha and beta proteins (a+b)	Profilin-like	GAF domain-like	automated matches	automated matches	(Stigmatella aurantiaca DW4/3-1 ) [TaxId: 378806 ],	SCOPe (2.08)
A	d4rq9a1	Alpha and beta proteins (a+b)	Profilin-like	PYP-like sensor domain (PAS domain)	automated matches	automated matches	(Stigmatella aurantiaca DW4/3-1 ) [TaxId: 378806 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PAS_2	e4rq9A1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_2	ECOD (1.6)
A	GAF	e4rq9A2	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Photoreceptor-histidine kinase BphP	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 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	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	IPR013515	Phytochrome, central region	Domain
A	IPR036097	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily	Homologous Superfamily
A	IPR043150	Phytochrome, PHY domain superfamily	Homologous Superfamily
A	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A	IPR003661	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain	Domain
A	IPR013654	PAS fold-2	Domain
A	IPR035965	PAS domain superfamily	Homologous Superfamily
A	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
A	IPR005467	Histidine kinase domain	Domain
A	IPR050351	Bacteriophytochrome/Sensor protein kinase WalK/GraS-like	Family
A	IPR003018	GAF domain	Domain
A	IPR029016	GAF-like domain superfamily	Homologous Superfamily
A	IPR001294	Phytochrome	Family
A	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.