3ZDS | pdb_00003zds

Structure of homogentisate 1,2-dioxygenase in complex with reaction intermediates of homogentisate with oxygen.

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)
L	d3zdsl_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
K	d3zdsk_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
J	d3zdsj_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
I	d3zdsi_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
H	d3zdsh_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
G	d3zdsg_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
F	d3zdsf_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
E	d3zdse_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
D	d3zdsd_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
C	d3zdsc_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
B	d3zdsb_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	automated matches	automated matches	(Pseudomonas putida KT2440 ) [TaxId: 160488 ],	SCOPe (2.08)
A	d3zdsa_	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)
L	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RmlC-like cupins	8088133	3001825	SCOP2B (2022-06-29)
B	SCOP2 Family	Homogentisate dioxygenase	8088132	4002879	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	RmlC-like cupins	8088133	3001825	SCOP2 (2022-06-29)
A	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)
L	HgmA_2nd	e3zdsL3	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	e3zdsL2	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	e3zdsK3	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	e3zdsK2	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	e3zdsJ3	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	e3zdsJ2	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	e3zdsI3	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	e3zdsI2	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	e3zdsH3	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	e3zdsH2	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	e3zdsG3	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	e3zdsG2	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	e3zdsF3	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	e3zdsF2	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	e3zdsE3	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	e3zdsE2	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	e3zdsD3	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	e3zdsD2	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	e3zdsC3	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	e3zdsC2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: HgmA_1st	ECOD (1.6)
B	HgmA_2nd	e3zdsB3	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	e3zdsB2	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	e3zdsA3	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	e3zdsA2	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)
L	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)
J	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)
H	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)
F	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)
D	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)
B	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)

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 arrangeme ...	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 arrangeme ...	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 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 DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA 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 carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process L-phenylalanine catabolic process aromatic amino acid metabolic process L-amino acid catabolic process carboxylic acid metabolic process L-amino acid metabolic process L-phenylalanine metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process small molecule catabolic process L-tyrosine catabolic process tyrosine metabolic 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