1SZR

A Dimer interface mutant of ornithine decarboxylase reveals structure of gem diamine intermediate

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth C]	d1szrc1	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 brucei ) [TaxId: 5702 ],	SCOPe (2.08)
A [auth C]	d1szrc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Eukaryotic ornithine decarboxylase	(Trypanosoma brucei brucei ) [TaxId: 5702 ],	SCOPe (2.08)
B [auth D]	d1szrd1	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 brucei ) [TaxId: 5702 ],	SCOPe (2.08)
B [auth D]	d1szrd2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Eukaryotic ornithine decarboxylase	(Trypanosoma brucei brucei ) [TaxId: 5702 ],	SCOPe (2.08)
C [auth A]	d1szra1	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 brucei ) [TaxId: 5702 ],	SCOPe (2.08)
C [auth A]	d1szra2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Eukaryotic ornithine decarboxylase	(Trypanosoma brucei brucei ) [TaxId: 5702 ],	SCOPe (2.08)
D [auth B]	d1szrb1	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 brucei ) [TaxId: 5702 ],	SCOPe (2.08)
D [auth B]	d1szrb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	PLP-binding barrel	Alanine racemase-like, N-terminal domain	Eukaryotic ornithine decarboxylase	(Trypanosoma brucei brucei ) [TaxId: 5702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth C]	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8042331	3001044	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8042331	3001044	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	PLP-binding barrel	8043283	3000273	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	PLP-binding barrel	8043283	3000273	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8042331	3001044	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8042331	3001044	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8042331	3001044	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	PLP-binding barrel	8043283	3000273	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8042331	3001044	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8042331	3001044	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Alanine racemase C-terminal domain-like	8042331	3001044	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	PLP-binding barrel	8043283	3000273	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 [auth C]	Orn_DAP_Arg_deC_C	e1szrC4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
A [auth C]	Orn_DAP_Arg_deC_N	e1szrC3	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 [auth D]	Orn_DAP_Arg_deC_C	e1szrD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
B [auth D]	Orn_DAP_Arg_deC_N	e1szrD2	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 [auth A]	Orn_DAP_Arg_deC_C	e1szrA4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
C [auth A]	Orn_DAP_Arg_deC_N	e1szrA3	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 [auth B]	Orn_DAP_Arg_deC_C	e1szrB2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Orn_DAP_Arg_deC_C	ECOD (1.6)
D [auth B]	Orn_DAP_Arg_deC_N	e1szrB1	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 [auth C]	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
A [auth C]	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
B [auth D]	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
B [auth D]	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
C [auth A]	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
C [auth A]	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
D [auth B]	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
D [auth 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 [auth C], B [auth D], C [auth A], D [auth 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 [auth C], B [auth D], C [auth A], D [auth B]	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 [auth C], B [auth D], C [auth A], D [auth B]	Ornithine decarboxylase	ornithine decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	amine metabolic process biogenic amine biosynthetic process biosynthetic process amine biosynthetic process polyamine biosynthetic process metabolic process polyamine metabolic process biogenic amine metabolic process ornithine metabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process amine metabolic process biogenic amine biosynthetic process biosynthetic process amine biosynthetic process polyamine biosynthetic process metabolic process polyamine metabolic process biogenic amine metabolic process ornithine metabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process non-proteinogenic amino acid metabolic process putrescine biosynthetic process putrescine biosynthetic process from ornithine putrescine metabolic process small molecule metabolic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

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