4AQ6

substrate bound homogentisate 1,2-dioxygenase

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)
B	d4aq6b_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
C	d4aq6c_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
D	d4aq6d_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
E	d4aq6e_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
G	d4aq6g_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
H	d4aq6h_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
I	d4aq6i_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
L	d4aq6l_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
A	d4aq6a_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
F	d4aq6f_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
J	d4aq6j_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
K	d4aq6k_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	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)
B	HgmA_2nd	e4aq6B3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_2nd	ECOD (1.6)
B	HgmA_1st	e4aq6B2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_1st	ECOD (1.6)
C	HgmA_2nd	e4aq6C3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_2nd	ECOD (1.6)
C	HgmA_1st	e4aq6C2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_1st	ECOD (1.6)
D	HgmA_2nd	e4aq6D3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_2nd	ECOD (1.6)
D	HgmA_1st	e4aq6D2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_1st	ECOD (1.6)
E	HgmA_2nd	e4aq6E3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_2nd	ECOD (1.6)
E	HgmA_1st	e4aq6E2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_1st	ECOD (1.6)
G	HgmA_2nd	e4aq6G3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_2nd	ECOD (1.6)
G	HgmA_1st	e4aq6G2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_1st	ECOD (1.6)
H	HgmA_2nd	e4aq6H3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_2nd	ECOD (1.6)
H	HgmA_1st	e4aq6H2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_1st	ECOD (1.6)
I	HgmA_2nd	e4aq6I3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_2nd	ECOD (1.6)
I	HgmA_1st	e4aq6I2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_1st	ECOD (1.6)
L	HgmA_2nd	e4aq6L3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_2nd	ECOD (1.6)
L	HgmA_1st	e4aq6L2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_1st	ECOD (1.6)
A	HgmA_2nd	e4aq6A3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_2nd	ECOD (1.6)
A	HgmA_1st	e4aq6A2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_1st	ECOD (1.6)
F	HgmA_2nd	e4aq6F3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_2nd	ECOD (1.6)
F	HgmA_1st	e4aq6F2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_1st	ECOD (1.6)
J	HgmA_2nd	e4aq6J3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_2nd	ECOD (1.6)
J	HgmA_1st	e4aq6J2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_1st	ECOD (1.6)
K	HgmA_2nd	e4aq6K3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_2nd	ECOD (1.6)
K	HgmA_1st	e4aq6K2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
C	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
D	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
E	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
G	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
H	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
I	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
L	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
A	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
F	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
J	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
K	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF04209	Homogentisate 1,2-dioxygenase C-terminal (HgmA_C)	Homogentisate 1,2-dioxygenase C-terminal	Homogentisate dioxygenase cleaves the aromatic ring during the metabolic degradation of Phe and Tyr. Homogentisate dioxygenase deficiency causes alkaptonuria. The structure of homogentisate dioxygenase shows that the enzyme forms a hexamer arrangem ...	Homogentisate dioxygenase cleaves the aromatic ring during the metabolic degradation of Phe and Tyr. Homogentisate dioxygenase deficiency causes alkaptonuria. The structure of homogentisate dioxygenase shows that the enzyme forms a hexamer arrangement comprised of a dimer of trimers. The active site iron ion is coordinated near the interface between the trimers [1]. This entry represents the C-terminal active site domain.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF20510	Homogentisate 1,2-dioxygenase N-terminal (HgmA_N)	Homogentisate 1,2-dioxygenase N-terminal	Homogentisate dioxygenase cleaves the aromatic ring during the metabolic degradation of Phe and Tyr. Homogentisate dioxygenase deficiency causes alkaptonuria. The structure of homogentisate dioxygenase shows that the enzyme forms a hexamer arrangem ...	Homogentisate dioxygenase cleaves the aromatic ring during the metabolic degradation of Phe and Tyr. Homogentisate dioxygenase deficiency causes alkaptonuria. The structure of homogentisate dioxygenase shows that the enzyme forms a hexamer arrangement comprised of a dimer of trimers. The active site iron ion is coordinated near the interface between the trimers [1]. This entry represents the N-terminal domain which forms a jelly roll of beta-strands [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	HOMOGENTISATE 1,2-DIOXYGENASE	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding homogentisate 1,2-dioxygenase activity oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen oxidoreductase activity oxidoreductase activity, acting on single donors with incorporation of molecular oxygen catalytic activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding homogentisate 1,2-dioxygenase activity oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen oxidoreductase activity oxidoreductase activity, acting on single donors with incorporation of molecular oxygen catalytic activity dioxygenase activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process catabolic process oxoacid metabolic process aromatic amino acid family catabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process cellular catabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process L-phenylalanine catabolic process aromatic amino acid metabolic process carboxylic acid metabolic process L-amino acid catabolic process L-amino acid metabolic process L-phenylalanine metabolic process proteinogenic amino acid metabolic process erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process small molecule catabolic process tyrosine metabolic process tyrosine catabolic process	protein-containing complex protein-DNA complex cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR022950	Homogentisate 1,2-dioxygenase, bacterial	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR014710	RmlC-like jelly roll fold	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR046452	Homogentisate 1,2-dioxygenase, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR011051	RmlC-like cupin domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR046451	Homogentisate 1,2-dioxygenase, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR005708	Homogentisate 1,2-dioxygenase	Family