3DGE | pdb_00003dge

Structure of a histidine kinase-response regulator complex reveals insights into Two-component signaling and a novel cis-autophosphorylation mechanism

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)
C [auth B]	d3dgeb1	All alpha proteins	ROP-like	Homodimeric domain of signal transducing histidine kinase	automated matches	automated matches	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
C [auth B]	d3dgeb2	Alpha and beta proteins (a+b)	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	Histidine kinase	automated matches	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d3dgea1	All alpha proteins	ROP-like	Homodimeric domain of signal transducing histidine kinase	automated matches	automated matches	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d3dgea2	Alpha and beta proteins (a+b)	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	Histidine kinase	automated matches	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
D	d3dged_	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	automated matches	automated matches	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B [auth C]	d3dgec_	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	automated matches	automated matches	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth B]	SCOP2B Superfamily	Homodimeric domain of signal transducing histidine kinase	8039116	3001864	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8039118	3000091	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8039118	3000091	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Homodimeric domain of signal transducing histidine kinase	8039116	3001864	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	CheY-like	8072786	3001156	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	CheY-like	8072786	3001156	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)
C [auth B]		e3dgeB3	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: SH2	F:	ECOD (20:10:01)
A		e3dgeA1	A: Alpha-beta plaits	X: FAD-dependent thiol oxidase	H: FAD-dependent thiol oxidase	T: TetR_N	F:	ECOD (20:10:01)
D		e3dgeD1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: YgbB	F:	ECOD (20:10:01)
B [auth C]		e3dgeC1	A: Alpha-beta plaits	X: FAD-dependent thiol oxidase	H: FAD-dependent thiol oxidase	T: Peptidase_M4,Peptidase_M4_C	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth B]	1.10.287.130	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain	CATH (4.3.0)
C [auth B]	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
A	1.10.287.130	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain	CATH (4.3.0)
A	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
D	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
B [auth C]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	PF00512	His Kinase A (phospho-acceptor) domain (HisKA)	His Kinase A (phospho-acceptor) domain	Dimerisation and phospho-acceptor domain of histidine kinases.	Domain
A, C [auth B]	PF02518	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase (HATPase_c)	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase	This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.	Domain
B [auth C], D	PF00072	Response regulator receiver domain (Response_reg)	Response regulator receiver domain	This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B]	Sensor protein	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 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 cation binding metal ion binding molecular transducer activity histidine phosphotransfer kinase activity identical protein binding protein binding	cellular response to stimulus regulation of biological process phosphorelay signal transduction system regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication cellular process signal transduction	cell periphery cellular anatomical structure plasma membrane membrane
B [auth C], D	Response regulator	DNA binding binding nucleic acid binding molecular transducer activity phosphorelay response regulator activity cation binding ion binding metal ion binding small molecule binding	cellular response to stimulus regulation of biological process phosphorelay signal transduction system regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication cellular process signal transduction	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR004358	Signal transduction histidine kinase-related protein, C-terminal	Domain
A, C [auth B]	IPR036097	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily	Homologous Superfamily
A, C [auth B]	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A, C [auth B]	IPR003661	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain	Domain
A, C [auth B]	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
A, C [auth B]	IPR005467	Histidine kinase domain	Domain
B [auth C], D	IPR011006	CheY-like superfamily	Homologous Superfamily
B [auth C], D	IPR001789	Signal transduction response regulator, receiver domain	Domain
B [auth C], D	IPR050595	Bacterial response regulator	Family

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.