Annotations: 1ORD

CRYSTALLOGRAPHIC STRUCTURE OF A PLP-DEPENDENT ORNITHINE DECARBOXYLASE FROM LACTOBACILLUS 30A TO 3.1 ANGSTROMS RESOLUTION

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1orda1	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	Ornithine decarboxylase N-terminal 'wing' domain	Ornithine decarboxylase N-terminal 'wing' domain	(Lactobacillus sp. 30A ) [TaxId: 1593 ],	SCOPe (2.08)
A	d1orda2	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Ornithine decarboxylase major domain	Ornithine decarboxylase major domain	(Lactobacillus sp. 30A ) [TaxId: 1593 ],	SCOPe (2.08)
A	d1orda3	Alpha and beta proteins (a+b)	Ornithine decarboxylase C-terminal domain	Ornithine decarboxylase C-terminal domain	Ornithine decarboxylase C-terminal domain	Ornithine decarboxylase C-terminal domain	(Lactobacillus sp. 30A ) [TaxId: 1593 ],	SCOPe (2.08)
B	d1ordb1	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	Ornithine decarboxylase N-terminal 'wing' domain	Ornithine decarboxylase N-terminal 'wing' domain	(Lactobacillus sp. 30A ) [TaxId: 1593 ],	SCOPe (2.08)
B	d1ordb2	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Ornithine decarboxylase major domain	Ornithine decarboxylase major domain	(Lactobacillus sp. 30A ) [TaxId: 1593 ],	SCOPe (2.08)
B	d1ordb3	Alpha and beta proteins (a+b)	Ornithine decarboxylase C-terminal domain	Ornithine decarboxylase C-terminal domain	Ornithine decarboxylase C-terminal domain	Ornithine decarboxylase C-terminal domain	(Lactobacillus sp. 30A ) [TaxId: 1593 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ornithine decarboxylase C-terminal domain	8036224	3000629	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8032410	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CheY-like	8044105	3001156	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8032410	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CheY-like	8044105	3001156	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ornithine decarboxylase C-terminal domain	8036224	3000629	SCOP2B (2022-06-29)

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	e1ordA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: OKR_DC_1_C	ECOD (v294.1)
A	T2SSM	e1ordA2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: T2SSM	ECOD (v294.1)
A	B12-binding	e1ordA3	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v294.1)
A	Esterase	e1ordA4	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Esterase	ECOD (v294.1)
B	OKR_DC_1_C	e1ordB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: OKR_DC_1_C	ECOD (v294.1)
B	T2SSM	e1ordB2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: T2SSM	ECOD (v294.1)
B	B12-binding	e1ordB3	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v294.1)
B	Esterase	e1ordB4	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Esterase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		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)
B	3.40.50.220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	ORNITHINE DECARBOXYLASE	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding ornithine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	amino acid metabolic process primary metabolic process metabolic process cellular process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011006	CheY-like superfamily	Homologous Superfamily
A, B	IPR027464	Ornithine decarboxylase, N-terminal	Homologous Superfamily
A, B	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B	IPR011193	Ornithine/lysine/arginine decarboxylase	Family
A, B	IPR008286	Orn/Lys/Arg decarboxylase, C-terminal	Domain
A, B	IPR005308	Orn/Lys/Arg decarboxylase, N-terminal	Domain
A, B	IPR036633	Orn/Lys/Arg decarboxylase, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B	IPR000310	Orn/Lys/Arg decarboxylase, major domain	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	ornithine decarboxylase M-CSA #860	Catalyses the decarboxylation of ornithine to form putrescine. It belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase domain superfamily (fold I)	Defined by 3 residues: HIS:A-223ASP:A-316LYS:A-355 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.1.1.17 (PDB Primary Data) Search M-CSA Motif + EC 4.1.1.17

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.