4UPF | pdb_00004upf

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	OKR_DC_1_C	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: OKR_DC_1_C	ECOD (1.6)
A	OKR_DC_1_3rd	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: OKR_DC_1_3rd	ECOD (1.6)
A	OKR_DC_1_N	e4upfA1	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	e4upfA4	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)

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 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
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 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 alpha-amino acid catabolic process carboxylic acid catabolic process metabolic process cellular 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 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth D]	IPR045427	MoxR domain	Domain
B [auth D]	IPR050513	RavA family ATPases	Family
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
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

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.