Annotations: 1YKO

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ykoa_	All beta proteins	Prealbumin-like	Aromatic compound dioxygenase	Aromatic compound dioxygenase	Protocatechuate-3,4-dioxygenase, alpha chain	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
I	d1ykoi_	All beta proteins	Prealbumin-like	Aromatic compound dioxygenase	Aromatic compound dioxygenase	Protocatechuate-3,4-dioxygenase, alpha chain	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
C	d1ykoc_	All beta proteins	Prealbumin-like	Aromatic compound dioxygenase	Aromatic compound dioxygenase	Protocatechuate-3,4-dioxygenase, alpha chain	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
E	d1ykoe_	All beta proteins	Prealbumin-like	Aromatic compound dioxygenase	Aromatic compound dioxygenase	Protocatechuate-3,4-dioxygenase, alpha chain	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
G	d1ykog_	All beta proteins	Prealbumin-like	Aromatic compound dioxygenase	Aromatic compound dioxygenase	Protocatechuate-3,4-dioxygenase, alpha chain	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
K	d1ykok_	All beta proteins	Prealbumin-like	Aromatic compound dioxygenase	Aromatic compound dioxygenase	Protocatechuate-3,4-dioxygenase, alpha chain	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
B	d1ykob1	All beta proteins	Prealbumin-like	Aromatic compound dioxygenase	Aromatic compound dioxygenase	Protocatechuate-3,4-dioxygenase, beta chain	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
F	d1ykof_	All beta proteins	Prealbumin-like	Aromatic compound dioxygenase	Aromatic compound dioxygenase	Protocatechuate-3,4-dioxygenase, beta chain	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
H	d1ykoh_	All beta proteins	Prealbumin-like	Aromatic compound dioxygenase	Aromatic compound dioxygenase	Protocatechuate-3,4-dioxygenase, beta chain	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
J	d1ykoj_	All beta proteins	Prealbumin-like	Aromatic compound dioxygenase	Aromatic compound dioxygenase	Protocatechuate-3,4-dioxygenase, beta chain	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
L	d1ykol_	All beta proteins	Prealbumin-like	Aromatic compound dioxygenase	Aromatic compound dioxygenase	Protocatechuate-3,4-dioxygenase, beta chain	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
D	d1ykod_	All beta proteins	Prealbumin-like	Aromatic compound dioxygenase	Aromatic compound dioxygenase	Protocatechuate-3,4-dioxygenase, beta chain	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Aromatic compound dioxygenase	8040371	3000868	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Aromatic compound dioxygenase	8040371	3000868	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Aromatic compound dioxygenase	8040371	3000868	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Aromatic compound dioxygenase	8040371	3000868	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Aromatic compound dioxygenase	8040371	3000868	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Aromatic compound dioxygenase	8040371	3000868	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Aromatic compound dioxygenase	8032517	3000868	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Aromatic compound dioxygenase	8032517	3000868	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Aromatic compound dioxygenase	8032517	3000868	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Aromatic compound dioxygenase	8032517	3000868	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Aromatic compound dioxygenase	8032517	3000868	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Aromatic compound dioxygenase	8032517	3000868	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	PF00775	e1ykoA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: PF00775	ECOD (1.6)
I	PF00775	e1ykoI1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: PF00775	ECOD (1.6)
C	PF00775	e1ykoC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: PF00775	ECOD (1.6)
E	PF00775	e1ykoE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: PF00775	ECOD (1.6)
G	PF00775	e1ykoG2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: PF00775	ECOD (1.6)
K	PF00775	e1ykoK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: PF00775	ECOD (1.6)
B	PF00775,PF12391	e1ykoB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: PF00775,PF12391	ECOD (1.6)
F	PF00775,PF12391	e1ykoF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: PF00775,PF12391	ECOD (1.6)
H	PF00775,PF12391	e1ykoH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: PF00775,PF12391	ECOD (1.6)
J	PF00775,PF12391	e1ykoJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: PF00775,PF12391	ECOD (1.6)
L	PF00775,PF12391	e1ykoL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: PF00775,PF12391	ECOD (1.6)
D	PF00775,PF12391	e1ykoD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: PF00775,PF12391	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.130.10	Mainly Beta	Sandwich	Protocatechuate 3,4-Dioxygenase, subunit A	Aromatic compound dioxygenase	CATH (4.3.0)
I	2.60.130.10	Mainly Beta	Sandwich	Protocatechuate 3,4-Dioxygenase, subunit A	Aromatic compound dioxygenase	CATH (4.3.0)
C	2.60.130.10	Mainly Beta	Sandwich	Protocatechuate 3,4-Dioxygenase, subunit A	Aromatic compound dioxygenase	CATH (4.3.0)
E	2.60.130.10	Mainly Beta	Sandwich	Protocatechuate 3,4-Dioxygenase, subunit A	Aromatic compound dioxygenase	CATH (4.3.0)
G	2.60.130.10	Mainly Beta	Sandwich	Protocatechuate 3,4-Dioxygenase, subunit A	Aromatic compound dioxygenase	CATH (4.3.0)
K	2.60.130.10	Mainly Beta	Sandwich	Protocatechuate 3,4-Dioxygenase, subunit A	Aromatic compound dioxygenase	CATH (4.3.0)
B	2.60.130.10	Mainly Beta	Sandwich	Protocatechuate 3,4-Dioxygenase, subunit A	Aromatic compound dioxygenase	CATH (4.3.0)
F	2.60.130.10	Mainly Beta	Sandwich	Protocatechuate 3,4-Dioxygenase, subunit A	Aromatic compound dioxygenase	CATH (4.3.0)
H	2.60.130.10	Mainly Beta	Sandwich	Protocatechuate 3,4-Dioxygenase, subunit A	Aromatic compound dioxygenase	CATH (4.3.0)
J	2.60.130.10	Mainly Beta	Sandwich	Protocatechuate 3,4-Dioxygenase, subunit A	Aromatic compound dioxygenase	CATH (4.3.0)
L	2.60.130.10	Mainly Beta	Sandwich	Protocatechuate 3,4-Dioxygenase, subunit A	Aromatic compound dioxygenase	CATH (4.3.0)
D	2.60.130.10	Mainly Beta	Sandwich	Protocatechuate 3,4-Dioxygenase, subunit A	Aromatic compound dioxygenase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K	PF00775	Dioxygenase (Dioxygenase_C)	Dioxygenase	-	Domain
B, D, F, H, J B, D, F, H, J, L	PF12391	Protocatechuate 3,4-dioxygenase beta subunit N terminal (PCDO_beta_N)	Protocatechuate 3,4-dioxygenase beta subunit N terminal	-	Family
B, D, F, H, J B, D, F, H, J, L	PF00775	Dioxygenase (Dioxygenase_C)	Dioxygenase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K	Protocatechuate 3,4-dioxygenase alpha chain	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen oxidoreductase activity protocatechuate 3,4-dioxygenase activity oxidoreductase activity, acting on single donors with incorporation of molecular oxygen catalytic activity dioxygenase activity cation binding ferric iron binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding	catabolic process beta-ketoadipate pathway metabolic process	-
B, D, F, H, J B, D, F, H, J, L	Protocatechuate 3,4-dioxygenase beta chain	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen oxidoreductase activity protocatechuate 3,4-dioxygenase activity oxidoreductase activity, acting on single donors with incorporation of molecular oxygen catalytic activity dioxygenase activity cation binding ferric iron binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding	catabolic process oxoacid metabolic process organic hydroxy compound metabolic process catechol-containing compound metabolic process organic acid metabolic process organic acid catabolic process cellular catabolic process organic substance metabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule metabolic process 3,4-dihydroxybenzoate catabolic process 3,4-dihydroxybenzoate metabolic process benzene-containing compound metabolic process catabolic process oxoacid metabolic process organic hydroxy compound metabolic process catechol-containing compound metabolic process organic acid metabolic process organic acid catabolic process cellular catabolic process organic substance metabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule metabolic process 3,4-dihydroxybenzoate catabolic process 3,4-dihydroxybenzoate metabolic process benzene-containing compound metabolic process catechol-containing compound catabolic process cellular metabolic process carboxylic acid metabolic process organic cyclic compound catabolic process phenol-containing compound catabolic process organic cyclic compound metabolic process organic hydroxy compound catabolic process phenol-containing compound metabolic process metabolic process cellular process monocarboxylic acid metabolic process small molecule catabolic process organic substance catabolic process beta-ketoadipate pathway	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K	IPR012786	Protocatechuate 3,4-dioxygenase, alpha subunit	Family
A, C, E, G, I A, C, E, G, I, K	IPR000627	Intradiol ring-cleavage dioxygenase, C-terminal	Domain
A, C, E, G, I A, C, E, G, I, K	IPR015889	Intradiol ring-cleavage dioxygenase, core	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR012785	Protocatechuate 3,4-dioxygenase, beta subunit	Family
B, D, F, H, J B, D, F, H, J, L	IPR000627	Intradiol ring-cleavage dioxygenase, C-terminal	Domain
B, D, F, H, J B, D, F, H, J, L	IPR024756	Protocatechuate 3,4-dioxygenase beta subunit, N-terminal	Domain
B, D, F, H, J B, D, F, H, J, L	IPR015889	Intradiol ring-cleavage dioxygenase, core	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.