3KP0

Crystal Structure of ORNITHINE 4,5 AMINOMUTASE in complex with 2,4-diaminobutyrate (DAB) (Aerobic)

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth E]	SCOP2B Superfamily	OraS globular domain-like	8092026	3002551	SCOP2B (2022-06-29)
D [auth F]	SCOP2B Superfamily	OraS globular domain-like	8092026	3002551	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	OraS globular domain-like	8092026	3002551	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	OraS globular domain-like	8092026	3002551	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)
C [auth B]	OAM_dimer_1	e3kp0B5	A: a+b two layers	X: Dodecin subunit-like	H: D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain (From Topology)	T: D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain	F: OAM_dimer_1	ECOD (1.6)
C [auth B]	Lys-AminoMut_A_2nd	e3kp0B3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Lys-AminoMut_A_2nd	ECOD (1.6)
C [auth B]	B12-binding	e3kp0B1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)
E [auth C]	OAM_dimer_1	e3kp0C5	A: a+b two layers	X: Dodecin subunit-like	H: D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain (From Topology)	T: D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain	F: OAM_dimer_1	ECOD (1.6)
E [auth C]	Lys-AminoMut_A_2nd	e3kp0C3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Lys-AminoMut_A_2nd	ECOD (1.6)
E [auth C]	B12-binding	e3kp0C1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)
A	OAM_dimer_1	e3kp0A1	A: a+b two layers	X: Dodecin subunit-like	H: D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain (From Topology)	T: D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain	F: OAM_dimer_1	ECOD (1.6)
A	Lys-AminoMut_A_2nd	e3kp0A2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Lys-AminoMut_A_2nd	ECOD (1.6)
G [auth D]	OAM_dimer_1	e3kp0D3	A: a+b two layers	X: Dodecin subunit-like	H: D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain (From Topology)	T: D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain	F: OAM_dimer_1	ECOD (1.6)
G [auth D]	Lys-AminoMut_A_2nd	e3kp0D4	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Lys-AminoMut_A_2nd	ECOD (1.6)
B [auth E]	OAM_alpha	e3kp0E1	A: alpha arrays	X: D-ornithine aminomutase S component-related (From Topology)	H: D-ornithine aminomutase S component-related (From Topology)	T: D-ornithine aminomutase S component-related	F: OAM_alpha	ECOD (1.6)
D [auth F]	OAM_alpha	e3kp0F1	A: alpha arrays	X: D-ornithine aminomutase S component-related (From Topology)	H: D-ornithine aminomutase S component-related (From Topology)	T: D-ornithine aminomutase S component-related	F: OAM_alpha	ECOD (1.6)
F [auth G]	OAM_alpha	e3kp0G1	A: alpha arrays	X: D-ornithine aminomutase S component-related (From Topology)	H: D-ornithine aminomutase S component-related (From Topology)	T: D-ornithine aminomutase S component-related	F: OAM_alpha	ECOD (1.6)
H	OAM_alpha	e3kp0H1	A: alpha arrays	X: D-ornithine aminomutase S component-related (From Topology)	H: D-ornithine aminomutase S component-related (From Topology)	T: D-ornithine aminomutase S component-related	F: OAM_alpha	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth B]	3.20.20.440	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	D-Lysine 5,6-aminomutase alpha subunit	CATH (4.3.0)
C [auth B]	3.30.30.60	Alpha Beta	2-Layer Sandwich	Defensin A-like	D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain	CATH (4.3.0)
C [auth B]	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (4.3.0)
E [auth C]	3.20.20.440	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	D-Lysine 5,6-aminomutase alpha subunit	CATH (4.3.0)
E [auth C]	3.30.30.60	Alpha Beta	2-Layer Sandwich	Defensin A-like	D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain	CATH (4.3.0)
E [auth C]	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (4.3.0)
A	3.20.20.440	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	D-Lysine 5,6-aminomutase alpha subunit	CATH (4.3.0)
A	3.30.30.60	Alpha Beta	2-Layer Sandwich	Defensin A-like	D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain	CATH (4.3.0)
G [auth D]	3.20.20.440	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	D-Lysine 5,6-aminomutase alpha subunit	CATH (4.3.0)
G [auth D]	3.30.30.60	Alpha Beta	2-Layer Sandwich	Defensin A-like	D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain	CATH (4.3.0)
B [auth E]	6.10.250.2220	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B [auth E]	1.10.8.1000	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
D [auth F]	6.10.250.2220	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
D [auth F]	1.10.8.1000	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
F [auth G]	6.10.250.2220	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
F [auth G]	1.10.8.1000	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
H	6.10.250.2220	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
H	1.10.8.1000	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B], E [auth C], G [auth D]	PF09043	D-Lysine 5,6-aminomutase TIM-barrel domain of alpha subunit (Lys-AminoMut_A)	D-Lysine 5,6-aminomutase TIM-barrel domain of alpha subunit	Members of his family are involved in the 1,2 rearrangement of the terminal amino group of DL-lysine and of L-beta-lysine, using adenosylcobalamin (AdoCbl) and pyridoxal-5'-phosphate as co-factors. The structure is predominantly a PLP-binding TIM ba ...	Members of his family are involved in the 1,2 rearrangement of the terminal amino group of DL-lysine and of L-beta-lysine, using adenosylcobalamin (AdoCbl) and pyridoxal-5'-phosphate as co-factors. The structure is predominantly a PLP-binding TIM barrel domain, with several additional alpha-helices and beta-strands at the N and C termini. These helices and strands form an intertwined accessory clamp structure that wraps around the sides of the TIM barrel and extends up toward the Ado ligand of the Cbl co-factor, providing most of the interactions observed between the protein and the Ado ligand of the Cbl, suggesting that its role is mainly in stabilising AdoCbl in the precatalytic resting state [1]. This is a TIM-barrel domain.	Domain
A, C [auth B], E [auth C], G [auth D]	PF16554	Dimerisation domain of d-ornithine 4,5-aminomutase (OAM_dimer)	Dimerisation domain of d-ornithine 4,5-aminomutase	This family is the short dimerisation domain of the enzyme D-ornithine 4,5-aminomutase. It sits between the TIM-barrel Pfam:PF09043 and Pfam:PF02310. The enzyme is an alpha2-beta2-heterodimer that converts D-ornithine to 2,4-diaminopentanoic acid by ...	This family is the short dimerisation domain of the enzyme D-ornithine 4,5-aminomutase. It sits between the TIM-barrel Pfam:PF09043 and Pfam:PF02310. The enzyme is an alpha2-beta2-heterodimer that converts D-ornithine to 2,4-diaminopentanoic acid by way of radical propagation from an adenosylcobalamin to a pyridoxal 5'-phosphate cofactor [1].	Domain
A, C [auth B], E [auth C], G [auth D]	PF02310	B12 binding domain (B12-binding)	B12 binding domain	This domain binds to B12 (adenosylcobamide)[1-3], it is found in several enzymes, such as glutamate mutase Swiss:Q05488, methionine synthase Swiss:Q99707 and methylmalonyl-CoA mutase Swiss:P22033. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, ...	This domain binds to B12 (adenosylcobamide)[1-3], it is found in several enzymes, such as glutamate mutase Swiss:Q05488, methionine synthase Swiss:Q99707 and methylmalonyl-CoA mutase Swiss:P22033. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding [2].	Domain
B [auth E], D [auth F], F [auth G], H	PF16552	D-ornithine 4,5-aminomutase alpha-subunit (OAM_alpha)	D-ornithine 4,5-aminomutase alpha-subunit	OAM_alpha is the 12.8kDa, alpha subunit of d-ornithine 4,5-aminomutase, or OAM, an enzyme that converts d-ornithine to 2,4-diaminopentanoic acid by way of radical propagation from an adenosylcobalamin to a pyridoxal 5'-phosphate cofactor. OAM is an a ...	OAM_alpha is the 12.8kDa, alpha subunit of d-ornithine 4,5-aminomutase, or OAM, an enzyme that converts d-ornithine to 2,4-diaminopentanoic acid by way of radical propagation from an adenosylcobalamin to a pyridoxal 5'-phosphate cofactor. OAM is an alpha2-beta2 heterodimer comprising two strongly associating subunits. The packing of the alpha subunits against the beta helps to form the substrate and co-factor binding-regions [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B], E [auth C], G [auth D]	D-ornithine aminomutase E component	isomerase activity intramolecular aminotransferase activity catalytic activity D-ornithine 4,5-aminomutase activity intramolecular transferase activity vitamin binding binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding small molecule binding protein binding protein dimerization activity isomerase activity intramolecular aminotransferase activity catalytic activity D-ornithine 4,5-aminomutase activity intramolecular transferase activity vitamin binding binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding small molecule binding protein binding protein dimerization activity cation binding ion binding metal ion binding	-	-
B [auth E], D [auth F], F [auth G], H	D-ornithine aminomutase S component	isomerase activity intramolecular aminotransferase activity catalytic activity D-ornithine 4,5-aminomutase activity intramolecular transferase activity vitamin binding binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B], E [auth C], G [auth D]	IPR036724	Cobalamin-binding domain superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR015130	D-Lysine 5,6-aminomutase alpha subunit	Domain
A, C [auth B], E [auth C], G [auth D]	IPR006158	Cobalamin (vitamin B12)-binding domain	Domain
A, C [auth B], E [auth C], G [auth D]	IPR028991	D-lysine 5,6-aminomutase beta subunit KamE, N-terminal	Domain
A, C [auth B], E [auth C], G [auth D]	IPR037086	D-Lysine 5,6-aminomutase alpha subunit superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR036843	D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR016176	Cobalamin (vitamin B12)-dependent enzyme, catalytic	Homologous Superfamily
B [auth E], D [auth F], F [auth G], H	IPR015130	D-Lysine 5,6-aminomutase alpha subunit	Domain
B [auth E], D [auth F], F [auth G], H	IPR016176	Cobalamin (vitamin B12)-dependent enzyme, catalytic	Homologous Superfamily

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.