3NZQ

Crystal Structure of Biosynthetic arginine decarboxylase ADC (SpeA) from Escherichia coli, Northeast Structural Genomics Consortium Target ER600

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	e3nzqA4	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	e3nzqA2	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	e3nzqA1	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	ECOD (1.6)
A	Orn_DAP_Arg_deC_N	e3nzqA3	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	e3nzqB1	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	e3nzqB2	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	e3nzqB4	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	ECOD (1.6)
B	Orn_DAP_Arg_deC_N	e3nzqB3	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	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	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	Biosynthetic arginine decarboxylase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding organic cyclic compound binding anion binding heterocyclic compound binding arginine decarboxylase activity carboxy-lyase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding organic cyclic compound binding anion binding heterocyclic compound binding arginine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity identical protein binding protein 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 protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular process cellular component organization or biogenesis putrescine biosynthetic process putrescine 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 small molecule catabolic process organic substance catabolic process putrescine biosynthetic process from arginine	periplasmic space cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029066	PLP-binding barrel	Homologous Superfamily
A, B	IPR002985	Arginine decarboxylase	Family
A, B	IPR041128	Arginine decarboxylase, C-terminal helical	Domain
A, B	IPR022644	Orn/DAP/Arg decarboxylase 2, N-terminal	Domain
A, B	IPR022653	Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site	Binding Site
A, B	IPR040634	Arginine decarboxylase, helical bundle domain	Domain
A, B	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal	Homologous Superfamily
A, B	IPR000183	Ornithine/DAP/Arg decarboxylase	Family
A, B	IPR022657	Orn/DAP/Arg decarboxylase 2, conserved site	Conserved Site

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.