2PHD | pdb_00002phd

Crystal Structure Determination of a Salicylate 1,2-Dioxygenase from Pseudaminobacter salicylatoxidans

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)
A	d2phda1	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	Gentisate 1,2-dioxygenase-like	Gentisate 1,2-dioxygenase	(Pseudaminobacter salicylatoxidans ) [TaxId: 93369 ],	SCOPe (2.08)
B	d2phdb_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	Gentisate 1,2-dioxygenase-like	automated matches	(Pseudaminobacter salicylatoxidans ) [TaxId: 93369 ],	SCOPe (2.08)
C	d2phdc_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	Gentisate 1,2-dioxygenase-like	automated matches	(Pseudaminobacter salicylatoxidans ) [TaxId: 93369 ],	SCOPe (2.08)
D	d2phdd_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	Gentisate 1,2-dioxygenase-like	automated matches	(Pseudaminobacter salicylatoxidans ) [TaxId: 93369 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Gentisate 1, 2-dioxygenase-like	8023254	4001924	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RmlC-like cupins	8035634	3001825	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	RmlC-like cupins	8035634	3001825	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RmlC-like cupins	8035634	3001825	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RmlC-like cupins	8035634	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)
A		e2phdA2	A: HTH	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cupin_2	F:	ECOD (20:10:01)
B		e2phdB2	A: POZ domain	X: POZ domain	H: POZ domain	T: DUF3228	F:	ECOD (20:10:01)
C		e2phdC2	A: POZ domain	X: POZ domain	H: POZ domain	T: DUF3228	F:	ECOD (20:10:01)
D		e2phdD2	A: POZ domain	X: POZ domain	H: POZ domain	T: DUF3228	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF07883	Cupin domain (Cupin_2)	Cupin domain	This family represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Gentisate 1,2-dioxygenase	oxidoreductase activity catalytic activity dioxygenase activity cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR011051	RmlC-like cupin domain superfamily	Homologous Superfamily
A, B, C, D	IPR013096	Cupin 2, conserved barrel	Domain
A, B, C, D	IPR047183	Gentisate 1,2-dioxygenase-like	Family
A, B, C, D	IPR014710	RmlC-like jelly roll fold	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.