4UPF

Assembly principles of the unique cage formed by the ATPase RavA hexamer and the lysine decarboxylase LdcI decamer

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	e4upfA3	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	e4upfA2	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	e4upfA1	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	e4upfA4	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	PF01276	Orn/Lys/Arg decarboxylase, major domain (OKR_DC_1)	Orn/Lys/Arg decarboxylase, major domain	-	Domain
A	PF03711	Orn/Lys/Arg decarboxylase, C-terminal domain (OKR_DC_1_C)	Orn/Lys/Arg decarboxylase, C-terminal domain	-	Domain
B [auth D]	PF20265	ATPase, RavA, LARA domain (LARA_dom)	ATPase, RavA, LARA domain	This is the LARA (LdcI Associating domain of RavA) domain of bacterial regulatory ATPase RavA (Regulatory ATPase variant A) [1,2]. It adopts an unique fold which consists of a compact antiparallel beta-barrel- like structure formed by six beta-strand ...	This is the LARA (LdcI Associating domain of RavA) domain of bacterial regulatory ATPase RavA (Regulatory ATPase variant A) [1,2]. It adopts an unique fold which consists of a compact antiparallel beta-barrel- like structure formed by six beta-strands and one alpha-helix [1,2]. This domain mediates the interaction between RavA and LdcI (inducible lysine decarboxylase) which form a cage-like complex proposed to assist assembly of specific respiratory complexes in E. coli [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	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
B [auth D]	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	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A	IPR011193	Ornithine/lysine/arginine decarboxylase	Family
A	IPR008286	Orn/Lys/Arg decarboxylase, C-terminal	Domain
A	IPR005308	Orn/Lys/Arg decarboxylase, N-terminal	Domain
A	IPR036633	Orn/Lys/Arg decarboxylase, C-terminal domain superfamily	Homologous Superfamily
A	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A	IPR000310	Orn/Lys/Arg decarboxylase, major domain	Domain
B [auth D]	IPR045427	MoxR domain	Domain
B [auth D]	IPR046898	ATPase RavA, LARA domain	Domain
B [auth D]	IPR046932	ATPase RavA, LARA domain superfamily	Homologous Superfamily
B [auth D]	IPR023671	ATPase RavA	Family
B [auth D]	IPR003593	AAA+ ATPase domain	Domain
B [auth D]	IPR022547	ATPase, RavA, C-terminal	Domain
B [auth D]	IPR041538	ATPase RavA-like, AAA lid domain	Domain
B [auth D]	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 R01GM133198.