1YKP | pdb_00001ykp

Protocatechuate 3,4-Dioxygenase Y408H mutant bound to DHB

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d1ykpa_	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	d1ykpc_	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	d1ykpg_	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	d1ykpk_	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	d1ykpi_	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	d1ykpe_	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	d1ykpb_	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	d1ykpf_	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	d1ykpl_	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	d1ykpj_	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	d1ykph_	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	d1ykpd_	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)
C	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)
I	SCOP2B Superfamily	Aromatic compound dioxygenase	8040371	3000868	SCOP2B (2022-06-29)
E	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)
L	SCOP2B Superfamily	Aromatic compound dioxygenase	8032517	3000868	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Aromatic compound dioxygenase	8032517	3000868	SCOP2B (2022-06-29)
H	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	CBM_2	e1ykpA1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: CBM_2	ECOD (develop294)
C	CBM_2	e1ykpC1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: CBM_2	ECOD (develop294)
G	CBM_2	e1ykpG1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: CBM_2	ECOD (develop294)
K	CBM_2	e1ykpK1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: CBM_2	ECOD (develop294)
I	CBM_2	e1ykpI1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: CBM_2	ECOD (develop294)
E	CBM_2	e1ykpE1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: CBM_2	ECOD (develop294)
B	CBM_2	e1ykpB1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: CBM_2	ECOD (develop294)
F	CBM_2	e1ykpF1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: CBM_2	ECOD (develop294)
L	CBM_2	e1ykpL1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: CBM_2	ECOD (develop294)
J	CBM_2	e1ykpJ1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: CBM_2	ECOD (develop294)
H	CBM_2	e1ykpH1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: CBM_2	ECOD (develop294)
D	CBM_2	e1ykpD1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: CBM_2	ECOD (develop294)

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)
C	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)
I	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)
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)
L	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)
H	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)

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 cellular 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 3,4-dihydroxybenzoate metabolic process benzene-containing compound metabolic process oxoacid metabolic process catechol-containing compound catabolic process carboxylic acid metabolic process catechol-containing compound metabolic process organic acid metabolic process organic acid catabolic process phenol-containing compound catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process phenol-containing compound metabolic process metabolic process catabolic process 3,4-dihydroxybenzoate metabolic process benzene-containing compound metabolic process oxoacid metabolic process catechol-containing compound catabolic process carboxylic acid metabolic process catechol-containing compound metabolic process organic acid metabolic process organic acid catabolic process phenol-containing compound catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process phenol-containing compound metabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process 3,4-dihydroxybenzoate catabolic process small molecule 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	IPR050770	Intradiol Ring-Cleavage Dioxygenase	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	IPR050770	Intradiol Ring-Cleavage Dioxygenase	Family
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 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.