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	OKR_DC_1_C	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: OKR_DC_1_C	ECOD (1.6)
A	OKR_DC_1_3rd	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: OKR_DC_1_3rd	ECOD (1.6)
A	OKR_DC_1_N	e4upbA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: OKR_DC_1_N	ECOD (1.6)
A	OKR_DC_1_N2	e4upbA4	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: OKR_DC_1_N2	ECOD (1.6)
B	OKR_DC_1_C	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: OKR_DC_1_C	ECOD (1.6)
B	OKR_DC_1_3rd	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: OKR_DC_1_3rd	ECOD (1.6)
B	OKR_DC_1_N	e4upbB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: OKR_DC_1_N	ECOD (1.6)
B	OKR_DC_1_N2	e4upbB4	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: OKR_DC_1_N2	ECOD (1.6)
C	PRK13531_2nd	e4upbC2	A: beta barrels	X: LARA domain (From Topology)	H: LARA domain (From Topology)	T: LARA domain	F: PRK13531_2nd	ECOD (1.6)
C	PRK13531_1st	e4upbC1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PRK13531_1st	ECOD (1.6)
C	DUF3763	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: DUF3763	ECOD (1.6)
C	Sigma54_activat	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: Sigma54_activat	ECOD (1.6)
D	PRK13531_2nd	e4upbD1	A: beta barrels	X: LARA domain (From Topology)	H: LARA domain (From Topology)	T: LARA domain	F: PRK13531_2nd	ECOD (1.6)
D	PRK13531_1st	e4upbD2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PRK13531_1st	ECOD (1.6)
D	DUF3763	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: DUF3763	ECOD (1.6)
D	Sigma54_activat	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: Sigma54_activat	ECOD (1.6)
E	PRK13531_2nd	e4upbE2	A: beta barrels	X: LARA domain (From Topology)	H: LARA domain (From Topology)	T: LARA domain	F: PRK13531_2nd	ECOD (1.6)
E	PRK13531_1st	e4upbE3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PRK13531_1st	ECOD (1.6)
E	DUF3763	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: DUF3763	ECOD (1.6)
E	Sigma54_activat	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: Sigma54_activat	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 anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding guanosine tetraphosphate binding guanyl nucleotide binding binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide 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 lysine catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process cellular catabolic process alpha-amino acid catabolic process carboxylic acid catabolic process metabolic process lysine metabolic process catabolic process lysine catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process cellular catabolic process alpha-amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process small molecule catabolic process amino acid catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
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 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 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	-	cellular anatomical structure intracellular anatomical structure cytoplasm 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	IPR050513	RavA family ATPases	Family
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

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.

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