3N2O

X-ray crystal structure of arginine decarboxylase complexed with Arginine from Vibrio vulnificus

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)
A	Orn_DAP_Arg_deC_C	e3n2oA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
A	SpeA_1st	e3n2oA3	A: alpha bundles	X: Spectrin repeat-like	H: Helical bundle domain in arginine decarboxylase (From Topology)	T: Helical bundle domain in arginine decarboxylase	F: SpeA_1st	ECOD (1.6)
A	SpeA_2nd_1	e3n2oA4	A: alpha bundles	X: Arginine decarboxylase C-terminal helical extension (From Topology)	H: Arginine decarboxylase C-terminal helical extension (From Topology)	T: Arginine decarboxylase C-terminal helical extension	F: SpeA_2nd_1	ECOD (1.6)
A	Orn_DAP_Arg_deC_N	e3n2oA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Orn_DAP_Arg_deC_N	ECOD (1.6)
B	Orn_DAP_Arg_deC_C	e3n2oB2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
B	SpeA_1st	e3n2oB1	A: alpha bundles	X: Spectrin repeat-like	H: Helical bundle domain in arginine decarboxylase (From Topology)	T: Helical bundle domain in arginine decarboxylase	F: SpeA_1st	ECOD (1.6)
B	SpeA_2nd_1	e3n2oB3	A: alpha bundles	X: Arginine decarboxylase C-terminal helical extension (From Topology)	H: Arginine decarboxylase C-terminal helical extension (From Topology)	T: Arginine decarboxylase C-terminal helical extension	F: SpeA_2nd_1	ECOD (1.6)
B	Orn_DAP_Arg_deC_N	e3n2oB4	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Orn_DAP_Arg_deC_N	ECOD (1.6)
C	Orn_DAP_Arg_deC_C	e3n2oC4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
C	SpeA_1st	e3n2oC2	A: alpha bundles	X: Spectrin repeat-like	H: Helical bundle domain in arginine decarboxylase (From Topology)	T: Helical bundle domain in arginine decarboxylase	F: SpeA_1st	ECOD (1.6)
C	SpeA_2nd_1	e3n2oC1	A: alpha bundles	X: Arginine decarboxylase C-terminal helical extension (From Topology)	H: Arginine decarboxylase C-terminal helical extension (From Topology)	T: Arginine decarboxylase C-terminal helical extension	F: SpeA_2nd_1	ECOD (1.6)
C	Orn_DAP_Arg_deC_N	e3n2oC3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Orn_DAP_Arg_deC_N	ECOD (1.6)
D	Orn_DAP_Arg_deC_C	e3n2oD4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
D	SpeA_1st	e3n2oD3	A: alpha bundles	X: Spectrin repeat-like	H: Helical bundle domain in arginine decarboxylase (From Topology)	T: Helical bundle domain in arginine decarboxylase	F: SpeA_1st	ECOD (1.6)
D	SpeA_2nd_1	e3n2oD1	A: alpha bundles	X: Arginine decarboxylase C-terminal helical extension (From Topology)	H: Arginine decarboxylase C-terminal helical extension (From Topology)	T: Arginine decarboxylase C-terminal helical extension	F: SpeA_2nd_1	ECOD (1.6)
D	Orn_DAP_Arg_deC_N	e3n2oD2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Orn_DAP_Arg_deC_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
A	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
A	1.20.58.930	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
A	1.10.287.3440	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
B	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
B	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
B	1.20.58.930	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
B	1.10.287.3440	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
C	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
C	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
C	1.20.58.930	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
C	1.10.287.3440	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
D	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
D	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
D	1.20.58.930	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
D	1.10.287.3440	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF17810	Arginine decarboxylase helical bundle domain (Arg_decarb_HB)	Arginine decarboxylase helical bundle domain	This entry represents a helical bundle domain that is found between the two enzymatic domains of the arginine decarboxylases [1].	Domain
A, B, C, D	PF02784	Pyridoxal-dependent decarboxylase, pyridoxal binding domain (Orn_Arg_deC_N)	Pyridoxal-dependent decarboxylase, pyridoxal binding domain	These pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates This domain has a TIM barrel fold.	Domain
A, B, C, D	PF17944	Arginine decarboxylase C-terminal helical extension (Arg_decarbox_C)	Arginine decarboxylase C-terminal helical extension	This small three helical domain is found at the C-terminus of the arginine decarboxylase enzyme.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Biosynthetic arginine decarboxylase	arginine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity cation binding ion binding binding metal ion binding small molecule binding	organonitrogen compound metabolic process organonitrogen compound biosynthetic process polyamine metabolic process amine metabolic process biogenic amine biosynthetic process spermidine metabolic process organic substance metabolic process biosynthetic process amine biosynthetic process polyamine biosynthetic process organic substance biosynthetic process metabolic process spermidine biosynthetic process biogenic amine metabolic process organonitrogen compound metabolic process organonitrogen compound biosynthetic process polyamine metabolic process amine metabolic process biogenic amine biosynthetic process spermidine metabolic process organic substance metabolic process biosynthetic process amine biosynthetic process polyamine biosynthetic process organic substance biosynthetic process metabolic process spermidine biosynthetic process biogenic amine metabolic process catabolic process oxoacid metabolic process glutamine family amino acid catabolic process amino acid metabolic process arginine catabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process cellular catabolic process arginine metabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process organonitrogen compound catabolic process cellular metabolic process carboxylic acid metabolic process L-amino acid catabolic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process cellular process small molecule catabolic process organic substance catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR029066	PLP-binding barrel	Homologous Superfamily
A, B, C, D	IPR040634	Arginine decarboxylase, helical bundle domain	Domain
A, B, C, D	IPR002985	Arginine decarboxylase	Family
A, B, C, D	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal	Homologous Superfamily
A, B, C, D	IPR041128	Arginine decarboxylase, C-terminal helical	Domain
A, B, C, D	IPR000183	Ornithine/DAP/Arg decarboxylase	Family
A, B, C, D	IPR022644	Orn/DAP/Arg decarboxylase 2, N-terminal	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.