1NJJ

Crystal structure determination of T. brucei ornithine decarboxylase bound to D-ornithine and to G418

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1njja1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Alanine racemase C-terminal domain-like	Eukaryotic ODC-like	Eukaryotic ornithine decarboxylase (ODC)	(Trypanosoma brucei gambiense ) [TaxId: 31285 ],	SCOPe (2.08)
A	d1njja2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Eukaryotic ornithine decarboxylase	(Trypanosoma brucei gambiense ) [TaxId: 31285 ],	SCOPe (2.08)
B	d1njjb1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Alanine racemase C-terminal domain-like	Eukaryotic ODC-like	Eukaryotic ornithine decarboxylase (ODC)	(Trypanosoma brucei gambiense ) [TaxId: 31285 ],	SCOPe (2.08)
B	d1njjb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Eukaryotic ornithine decarboxylase	(Trypanosoma brucei gambiense ) [TaxId: 31285 ],	SCOPe (2.08)
C	d1njjc1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Alanine racemase C-terminal domain-like	Eukaryotic ODC-like	Eukaryotic ornithine decarboxylase (ODC)	(Trypanosoma brucei gambiense ) [TaxId: 31285 ],	SCOPe (2.08)
C	d1njjc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Eukaryotic ornithine decarboxylase	(Trypanosoma brucei gambiense ) [TaxId: 31285 ],	SCOPe (2.08)
D	d1njjd1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Alanine racemase C-terminal domain-like	Eukaryotic ODC-like	Eukaryotic ornithine decarboxylase (ODC)	(Trypanosoma brucei gambiense ) [TaxId: 31285 ],	SCOPe (2.08)
D	d1njjd2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Eukaryotic ornithine decarboxylase	(Trypanosoma brucei gambiense ) [TaxId: 31285 ],	SCOPe (2.08)

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	e1njjA2	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	e1njjA1	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	e1njjB4	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	e1njjB1	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	e1njjC2	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	e1njjC1	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	e1njjD1	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	e1njjD2	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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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	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	ornithine decarboxylase	ornithine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	ornithine metabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process polyamine metabolic process alpha-amino acid metabolic process non-proteinogenic amino acid metabolic process putrescine biosynthetic process amine metabolic process biogenic amine biosynthetic process biosynthetic process putrescine biosynthetic process from ornithine amine biosynthetic process ornithine metabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process polyamine metabolic process alpha-amino acid metabolic process non-proteinogenic amino acid metabolic process putrescine biosynthetic process amine metabolic process biogenic amine biosynthetic process biosynthetic process putrescine biosynthetic process from ornithine amine biosynthetic process polyamine biosynthetic process putrescine metabolic process metabolic process cellular process small molecule metabolic process biogenic amine metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002433	Ornithine decarboxylase	Family
A, B, C, D	IPR029066	PLP-binding barrel	Homologous Superfamily
A, B, C, D	IPR022643	Orn/DAP/Arg decarboxylase 2, C-terminal	Domain
A, B, C, D	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal	Homologous Superfamily
A, B, C, D	IPR000183	Ornithine/DAP/Arg decarboxylase	Family
A, B, C, D	IPR022644	Orn/DAP/Arg decarboxylase 2, N-terminal	Domain
A, B, C, D	IPR022653	Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site	Binding Site

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.