1NY5

Crystal structure of sigm54 activator (AAA+ ATPase) in the inactive state

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	d1ny5a1	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	CheY-related	Transcriptional activator sigm54 (NtrC1), N-terminal domain	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d1ny5a2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Transcriptional activator sigm54 (NtrC1), C-terminal domain	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
B	d1ny5b1	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	CheY-related	Transcriptional activator sigm54 (NtrC1), N-terminal domain	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
B	d1ny5b2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Transcriptional activator sigm54 (NtrC1), C-terminal domain	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	CheY-related	8024696	4003632	SCOP2 (2022-06-29)
A	SCOP2 Family	Extended AAA-ATPase domain	8024698	4000283	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	CheY-like	8037075	3001156	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RecA-like P-loop NTPases	8037077	3002019	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104150	3002834	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104150	3002834	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CheY-like	8037075	3001156	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8037077	3002019	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	AtoC	e1ny5A1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: AtoC	ECOD (1.6)
A	Sigma54_activat	e1ny5A2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
A	Response_reg	e1ny5A3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Response_reg	ECOD (1.6)
B	AtoC	e1ny5B1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: AtoC	ECOD (1.6)
B	Sigma54_activat	e1ny5B2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
B	Response_reg	e1ny5B3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Response_reg	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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
A, B	PF00158	Sigma-54 interaction domain (Sigma54_activat)	Sigma-54 interaction domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	transcriptional regulator (NtrC family)	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 pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity sequence-specific DNA binding DNA binding nucleic acid binding cation binding metal ion binding 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 cellular biosynthetic process RNA metabolic process regulation of primary metabolic process 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 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 cellular metabolic process 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 regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A, B	IPR011006	CheY-like superfamily	Homologous Superfamily
A, B	IPR002197	DNA binding HTH domain, Fis-type	Domain
A, B	IPR001789	Signal transduction response regulator, receiver domain	Domain
A, B	IPR002078	RNA polymerase sigma factor 54 interaction domain	Domain
A, B	IPR025662	Sigma-54 interaction domain, ATP-binding site 1	Binding Site
A, B	IPR003593	AAA+ ATPase domain	Domain
A, B	IPR025943	Sigma-54 interaction domain, ATP-binding site 2	Binding Site
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.