2NVA | pdb_00002nva

The X-ray crystal structure of the Paramecium bursaria Chlorella virus arginine decarboxylase bound to agmatine

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	e2nvaA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
A	Orn_DAP_Arg_deC_N	e2nvaA2	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	e2nvaC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
C	Orn_DAP_Arg_deC_N	e2nvaC2	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	e2nvaD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
D	Orn_DAP_Arg_deC_N	e2nvaD2	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)
E	Orn_DAP_Arg_deC_C	e2nvaE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
E	Orn_DAP_Arg_deC_N	e2nvaE2	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)
F	Orn_DAP_Arg_deC_C	e2nvaF1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
F	Orn_DAP_Arg_deC_N	e2nvaF2	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)
H	Orn_DAP_Arg_deC_C	e2nvaH1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
H	Orn_DAP_Arg_deC_N	e2nvaH2	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)
G	Orn_DAP_Arg_deC_C	e2nvaG1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
G	Orn_DAP_Arg_deC_N	e2nvaG2	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	e2nvaB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
B	Orn_DAP_Arg_deC_N	e2nvaB2	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)
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)
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)
E	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
E	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
F	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
F	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
H	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
H	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
G	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
G	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	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)

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	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, E A, B, C, D, E, F, G, H	PF00278	Pyridoxal-dependent decarboxylase, C-terminal sheet domain (Orn_DAP_Arg_deC)	Pyridoxal-dependent decarboxylase, C-terminal sheet domain	These pyridoxal-dependent decarboxylases act on ornithine, lysine, arginine and related substrates.	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	arginine decarboxylase, A207R protein	ornithine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	oxoacid metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process arginine metabolic process biogenic amine biosynthetic process putrescine metabolic process small molecule metabolic process putrescine biosynthetic process from arginine, via ornithine carboxylic acid metabolic process primary metabolic process polyamine metabolic process L-amino acid metabolic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process arginine metabolic process biogenic amine biosynthetic process putrescine metabolic process small molecule metabolic process putrescine biosynthetic process from arginine, via ornithine carboxylic acid metabolic process primary metabolic process polyamine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process putrescine biosynthetic process amine metabolic process biosynthetic process amine biosynthetic process polyamine biosynthetic process putrescine biosynthetic process from arginine metabolic process cellular process biogenic amine metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR002433	Ornithine decarboxylase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029066	PLP-binding barrel	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR022643	Orn/DAP/Arg decarboxylase 2, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000183	Ornithine/DAP/Arg decarboxylase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR022644	Orn/DAP/Arg decarboxylase 2, N-terminal	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.