4UPB

Electron cryo-microscopy of the complex formed between the hexameric ATPase RavA and the decameric inducible decarboxylase LdcI

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF03711	e4upbA3	A: a+b two layers	X: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: PF03711	ECOD (1.6)
A	PF01276	e4upbA2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: PF01276	ECOD (1.6)
A	PF03709	e4upbA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: PF03709	ECOD (1.6)
A	PF01276	e4upbA4	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: PF01276	ECOD (1.6)
B	PF03711	e4upbB3	A: a+b two layers	X: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: PF03711	ECOD (1.6)
B	PF01276	e4upbB2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: PF01276	ECOD (1.6)
B	PF03709	e4upbB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: PF03709	ECOD (1.6)
B	PF01276	e4upbB4	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: PF01276	ECOD (1.6)
C	PF20265	e4upbC2	A: beta barrels	X: LARA domain (From Topology)	H: LARA domain (From Topology)	T: LARA domain	F: PF20265	ECOD (1.6)
C	PF17868	e4upbC1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17868	ECOD (1.6)
C	PF12592	e4upbC3	A: alpha bundles	X: Spectrin repeat-like	H: Triple-helical domain in regulatory ATPase variant A (RavA) (From Topology)	T: Triple-helical domain in regulatory ATPase variant A (RavA)	F: PF12592	ECOD (1.6)
C	PF20030	e4upbC4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF20030	ECOD (1.6)
D	PF20265	e4upbD1	A: beta barrels	X: LARA domain (From Topology)	H: LARA domain (From Topology)	T: LARA domain	F: PF20265	ECOD (1.6)
D	PF17868	e4upbD2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17868	ECOD (1.6)
D	PF12592	e4upbD4	A: alpha bundles	X: Spectrin repeat-like	H: Triple-helical domain in regulatory ATPase variant A (RavA) (From Topology)	T: Triple-helical domain in regulatory ATPase variant A (RavA)	F: PF12592	ECOD (1.6)
D	PF20030	e4upbD3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF20030	ECOD (1.6)
E	PF20265	e4upbE2	A: beta barrels	X: LARA domain (From Topology)	H: LARA domain (From Topology)	T: LARA domain	F: PF20265	ECOD (1.6)
E	PF17868	e4upbE3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17868	ECOD (1.6)
E	PF12592	e4upbE1	A: alpha bundles	X: Spectrin repeat-like	H: Triple-helical domain in regulatory ATPase variant A (RavA) (From Topology)	T: Triple-helical domain in regulatory ATPase variant A (RavA)	F: PF12592	ECOD (1.6)
E	PF20030	e4upbE4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF20030	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03709	Orn/Lys/Arg decarboxylase, N-terminal domain (OKR_DC_1_N)	Orn/Lys/Arg decarboxylase, N-terminal domain	This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure.	Domain
A, B	PF01276	Orn/Lys/Arg decarboxylase, major domain (OKR_DC_1)	Orn/Lys/Arg decarboxylase, major domain	-	Domain
A, B	PF03711	Orn/Lys/Arg decarboxylase, C-terminal domain (OKR_DC_1_C)	Orn/Lys/Arg decarboxylase, C-terminal domain	-	Domain
C, D, E	PF07728	AAA domain (dynein-related subfamily) (AAA_5)	AAA domain (dynein-related subfamily)	This Pfam entry includes some of the AAA proteins not detected by the Pfam:PF00004 model.	Domain
C, D, E	PF12592	ATPase, RavA, C-terminal (ATPase_RavA_C)	ATPase, RavA, C-terminal	This domain is found at the C-terminal of bacterial regulatory ATPase RavA (Regulatory ATPase variant A) [1,2] and is the second subdomain that forms the discontinuous triple helical domain [1]. RavA forms an hexamer in which the triple helical domai ...	This domain is found at the C-terminal of bacterial regulatory ATPase RavA (Regulatory ATPase variant A) [1,2] and is the second subdomain that forms the discontinuous triple helical domain [1]. RavA forms an hexamer in which the triple helical domain mediates the lateral interactions between neighbouring RavA monomers [2].	Domain
C, D, E	PF17868	AAA lid domain (AAA_lid_8)	AAA lid domain	This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	LYSINE DECARBOXYLASE, INDUCIBLE	guanosine tetraphosphate binding guanyl nucleotide binding binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding guanosine tetraphosphate binding guanyl nucleotide binding binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding lysine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity identical protein binding protein binding	lysine metabolic process catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process cellular catabolic process organic substance metabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process lysine metabolic process catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process cellular catabolic process organic substance metabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process lysine catabolic process cellular metabolic process carboxylic acid metabolic process primary metabolic process alpha-amino acid catabolic process metabolic process cellular process small molecule catabolic process organic substance catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity
C, D, E	ATPASE RAVA	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 identical protein binding protein binding	-	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B	IPR011193	Ornithine/lysine/arginine decarboxylase	Family
A, B	IPR008286	Orn/Lys/Arg decarboxylase, C-terminal	Domain
A, B	IPR005308	Orn/Lys/Arg decarboxylase, N-terminal	Domain
A, B	IPR036633	Orn/Lys/Arg decarboxylase, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B	IPR000310	Orn/Lys/Arg decarboxylase, major domain	Domain
C, D, E	IPR045427	MoxR domain	Domain
C, D, E	IPR046898	ATPase RavA, LARA domain	Domain
C, D, E	IPR046932	ATPase RavA, LARA domain superfamily	Homologous Superfamily
C, D, E	IPR023671	ATPase RavA	Family
C, D, E	IPR003593	AAA+ ATPase domain	Domain
C, D, E	IPR022547	ATPase, RavA, C-terminal	Domain
C, D, E	IPR041538	ATPase RavA-like, AAA lid domain	Domain
C, D, E	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

Prepare Data

Validate Data

Deposit Data

Help and Resources

4UPB

Electron cryo-microscopy of the complex formed between the hexameric ATPase RavA and the decameric inducible decarboxylase LdcI

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage