2B9U | pdb_00002b9u

Crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase from sulfolobus tokodaii

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	d2b9ul_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	dTDP-sugar isomerase	dTDP-4-dehydrorhamnose 3,5-epimerase RmlC	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
K	d2b9uk_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	dTDP-sugar isomerase	dTDP-4-dehydrorhamnose 3,5-epimerase RmlC	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
J	d2b9uj_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	dTDP-sugar isomerase	dTDP-4-dehydrorhamnose 3,5-epimerase RmlC	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
I	d2b9ui_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	dTDP-sugar isomerase	dTDP-4-dehydrorhamnose 3,5-epimerase RmlC	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
H	d2b9uh_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	dTDP-sugar isomerase	dTDP-4-dehydrorhamnose 3,5-epimerase RmlC	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
G	d2b9ug_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	dTDP-sugar isomerase	dTDP-4-dehydrorhamnose 3,5-epimerase RmlC	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
F	d2b9uf_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	dTDP-sugar isomerase	dTDP-4-dehydrorhamnose 3,5-epimerase RmlC	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
E	d2b9ue_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	dTDP-sugar isomerase	dTDP-4-dehydrorhamnose 3,5-epimerase RmlC	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
D [auth B]	d2b9ub_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	dTDP-sugar isomerase	dTDP-4-dehydrorhamnose 3,5-epimerase RmlC	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
C [auth D]	d2b9ud_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	dTDP-sugar isomerase	dTDP-4-dehydrorhamnose 3,5-epimerase RmlC	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
B [auth C]	d2b9uc_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	dTDP-sugar isomerase	dTDP-4-dehydrorhamnose 3,5-epimerase RmlC	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
A	d2b9ua_	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	dTDP-sugar isomerase	dTDP-4-dehydrorhamnose 3,5-epimerase RmlC	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	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	8033089	3001825	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	RmlC-like cupins	8033089	3001825	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	RmlC-like cupins	8033089	3001825	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	RmlC-like cupins	8033089	3001825	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RmlC-like cupins	8033089	3001825	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RmlC-like cupins	8033089	3001825	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RmlC-like cupins	8033089	3001825	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RmlC-like cupins	8033089	3001825	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	RmlC-like cupins	8033089	3001825	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	RmlC-like cupins	8033089	3001825	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	RmlC-like cupins	8033089	3001825	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RmlC-like cupins	8033089	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	dTDP_sugar_isom	e2b9uL1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: dTDP_sugar_isom	ECOD (1.6)
K	dTDP_sugar_isom	e2b9uK1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: dTDP_sugar_isom	ECOD (1.6)
J	dTDP_sugar_isom	e2b9uJ1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: dTDP_sugar_isom	ECOD (1.6)
I	dTDP_sugar_isom	e2b9uI1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: dTDP_sugar_isom	ECOD (1.6)
H	dTDP_sugar_isom	e2b9uH1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: dTDP_sugar_isom	ECOD (1.6)
G	dTDP_sugar_isom	e2b9uG1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: dTDP_sugar_isom	ECOD (1.6)
F	dTDP_sugar_isom	e2b9uF1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: dTDP_sugar_isom	ECOD (1.6)
E	dTDP_sugar_isom	e2b9uE1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: dTDP_sugar_isom	ECOD (1.6)
D [auth B]	dTDP_sugar_isom	e2b9uB1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: dTDP_sugar_isom	ECOD (1.6)
C [auth D]	dTDP_sugar_isom	e2b9uD1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: dTDP_sugar_isom	ECOD (1.6)
B [auth C]	dTDP_sugar_isom	e2b9uC1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: dTDP_sugar_isom	ECOD (1.6)
A	dTDP_sugar_isom	e2b9uA1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: dTDP_sugar_isom	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 [auth B]	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
C [auth D]	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
B [auth C]	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 [auth C], C [auth D], D [auth B], E, A, B [auth C], C [auth D], D [auth B], E, F, G, H, I, J, K, L	PF00908	dTDP-4-dehydrorhamnose 3,5-epimerase (dTDP_sugar_isom)	dTDP-4-dehydrorhamnose 3,5-epimerase	This family catalyse the isomerisation of dTDP-4-dehydro-6-deoxy -D-glucose with dTDP-4-dehydro-6-deoxy-L-mannose. The EC number of this enzyme is 5.1.3.13.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C], C [auth D], D [auth B], E, A, B [auth C], C [auth D], D [auth B], E, F, G, H, I, J, K, L	hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase	isomerase activity racemase and epimerase activity dTDP-4-dehydrorhamnose 3,5-epimerase activity racemase and epimerase activity, acting on carbohydrates and derivatives catalytic activity	nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process nucleotide-sugar metabolic process carbohydrate derivative metabolic process primary metabolic process dTDP-rhamnose biosynthetic process nucleobase-containing compound biosynthetic process nucleobase-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process nucleotide-sugar metabolic process carbohydrate derivative metabolic process primary metabolic process dTDP-rhamnose biosynthetic process nucleobase-containing compound biosynthetic process nucleobase-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process nucleotide-sugar biosynthetic process phosphorus metabolic process carbohydrate metabolic process polysaccharide metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process macromolecule metabolic process macromolecule biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth D], D [auth B], E, A, B [auth C], C [auth D], D [auth B], E, F, G, H, I, J, K, L	IPR000888	dTDP-4-dehydrorhamnose 3,5-epimerase-like	Family
A, B [auth C], C [auth D], D [auth B], E, A, B [auth C], C [auth D], D [auth B], E, F, G, H, I, J, K, L	IPR011051	RmlC-like cupin domain superfamily	Homologous Superfamily
A, B [auth C], C [auth D], D [auth B], E, A, B [auth C], C [auth D], D [auth B], E, F, G, H, I, J, K, L	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.