1ORD | pdb_00001ord

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
Protein Family Annotation
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 two layers	X: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: OKR_DC_1_C	ECOD (1.6)
A	OKR_DC_1_3rd	e1ordA2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: OKR_DC_1_3rd	ECOD (1.6)
A	OKR_DC_1_N	e1ordA3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: OKR_DC_1_N	ECOD (1.6)
A	OKR_DC_1_N2	e1ordA4	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: OKR_DC_1_N2	ECOD (1.6)
B	OKR_DC_1_C	e1ordB1	A: a+b two layers	X: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: OKR_DC_1_C	ECOD (1.6)
B	OKR_DC_1_3rd	e1ordB2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: OKR_DC_1_3rd	ECOD (1.6)
B	OKR_DC_1_N	e1ordB3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: OKR_DC_1_N	ECOD (1.6)
B	OKR_DC_1_N2	e1ordB4	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: OKR_DC_1_N2	ECOD (1.6)

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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	PF01276	Orn/Lys/Arg decarboxylase, major domain (OKR_DC_1)	Orn/Lys/Arg decarboxylase, major domain		Domain
A, B	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	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

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.