2VYC | pdb_00002vyc

Crystal Structure of Acid Induced Arginine Decarboxylase from E. coli

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
J	RdRP_3	e2vycJ1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RdRP_3	ECOD (v294.1)
J	Response_reg	e2vycJ5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Response_reg	ECOD (v294.1)
I	RdRP_3	e2vycI1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RdRP_3	ECOD (v294.1)
I	Response_reg	e2vycI5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Response_reg	ECOD (v294.1)
H	Response_reg	e2vycH5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Response_reg	ECOD (v294.1)
G	Response_reg	e2vycG5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Response_reg	ECOD (v294.1)
F	RdRP_3	e2vycF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RdRP_3	ECOD (v294.1)
F	Response_reg	e2vycF5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Response_reg	ECOD (v294.1)
E	RdRP_3	e2vycE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RdRP_3	ECOD (v294.1)
E	Response_reg	e2vycE5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Response_reg	ECOD (v294.1)
D	RdRP_3	e2vycD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RdRP_3	ECOD (v294.1)
D	Response_reg	e2vycD5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Response_reg	ECOD (v294.1)
C	Response_reg	e2vycC5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Response_reg	ECOD (v294.1)
B	Response_reg	e2vycB5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Response_reg	ECOD (v294.1)
A	C1-set	e2vycA2	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: C1-set	ECOD (v294.1)
A	Response_reg	e2vycA5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Response_reg	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
J	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
J	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
J	3.90.100.10	Alpha Beta	Alpha-Beta Complex	Ornithine Decarboxylase	Chain A, domain 4	CATH (4.3.0)
I	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
I	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
I	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
I	3.90.100.10	Alpha Beta	Alpha-Beta Complex	Ornithine Decarboxylase	Chain A, domain 4	CATH (4.3.0)
H	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
H	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
H	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
H	3.90.100.10	Alpha Beta	Alpha-Beta Complex	Ornithine Decarboxylase	Chain A, domain 4	CATH (4.3.0)
G	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
G	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
G	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
G	3.90.100.10	Alpha Beta	Alpha-Beta Complex	Ornithine Decarboxylase	Chain A, domain 4	CATH (4.3.0)
F	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
F	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
F	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
F	3.90.100.10	Alpha Beta	Alpha-Beta Complex	Ornithine Decarboxylase	Chain A, domain 4	CATH (4.3.0)
E	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
E	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
E	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
E	3.90.100.10	Alpha Beta	Alpha-Beta Complex	Ornithine Decarboxylase	Chain A, domain 4	CATH (4.3.0)
D	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
D	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
D	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
D	3.90.100.10	Alpha Beta	Alpha-Beta Complex	Ornithine Decarboxylase	Chain A, domain 4	CATH (4.3.0)
C	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
C	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
C	3.90.100.10	Alpha Beta	Alpha-Beta Complex	Ornithine Decarboxylase	Chain A, domain 4	CATH (4.3.0)
B	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
B	3.90.100.10	Alpha Beta	Alpha-Beta Complex	Ornithine Decarboxylase	Chain A, domain 4	CATH (4.3.0)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
A	3.90.100.10	Alpha Beta	Alpha-Beta Complex	Ornithine Decarboxylase	Chain A, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	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, C, D, E A, B, C, D, E, F, G, H, I, J	PF01276	Orn/Lys/Arg decarboxylase, major domain (OKR_DC_1)	Orn/Lys/Arg decarboxylase, major domain		Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	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
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	BIODEGRADATIVE ARGININE DECARBOXYLASE	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding arginine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	catabolic process oxoacid metabolic process L-amino acid catabolic 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 L-amino acid metabolic process arginine metabolic process proteinogenic amino acid metabolic process L-arginine catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process catabolic process oxoacid metabolic process L-amino acid catabolic 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 L-amino acid metabolic process arginine metabolic process proteinogenic amino acid metabolic process L-arginine catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process small molecule catabolic process amino acid catabolic process homeostatic process biological regulation regulation of intracellular pH cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis regulation of pH monoatomic ion homeostasis intracellular chemical homeostasis regulation of biological quality monoatomic cation homeostasis intracellular pH elevation intracellular monoatomic ion homeostasis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR011193	Ornithine/lysine/arginine decarboxylase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR008286	Orn/Lys/Arg decarboxylase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR005308	Orn/Lys/Arg decarboxylase, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR036633	Orn/Lys/Arg decarboxylase, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR000310	Orn/Lys/Arg decarboxylase, major domain	Domain