1YWK | pdb_00001ywk

Crystal structure of 4-deoxy-1-threo-5-hexosulose-uronate ketol-isomerase from Enterococcus faecalis

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)
F	d1ywkf2	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	KduI-like	5-keto-4-deoxyuronate isomerase KduI	(Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)
F	d1ywkf3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)
E	d1ywke2	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	KduI-like	5-keto-4-deoxyuronate isomerase KduI	(Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)
E	d1ywke3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)
D	d1ywkd2	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	KduI-like	5-keto-4-deoxyuronate isomerase KduI	(Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)
D	d1ywkd3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)
C	d1ywkc2	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	KduI-like	5-keto-4-deoxyuronate isomerase KduI	(Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)
C	d1ywkc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)
B	d1ywkb2	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	KduI-like	5-keto-4-deoxyuronate isomerase KduI	(Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)
B	d1ywkb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)
A	d1ywka1	All beta proteins	Double-stranded beta-helix	RmlC-like cupins	KduI-like	5-keto-4-deoxyuronate isomerase KduI	(Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)
A	d1ywka2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Enterococcus faecalis ) [TaxId: 1351 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	RmlC-like cupins	8034991	3001825	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RmlC-like cupins	8034991	3001825	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RmlC-like cupins	8034991	3001825	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RmlC-like cupins	8034991	3001825	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RmlC-like cupins	8034991	3001825	SCOP2B (2022-06-29)
A	SCOP2 Family	KduI-like	8022611	4001894	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RmlC-like cupins	8034991	3001825	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	KduI_1	e1ywkF2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: KduI_1	ECOD (1.6)
E	KduI_1	e1ywkE1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: KduI_1	ECOD (1.6)
D	KduI_1	e1ywkD2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: KduI_1	ECOD (1.6)
C	KduI_1	e1ywkC2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: KduI_1	ECOD (1.6)
B	KduI_1	e1ywkB2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: KduI_1	ECOD (1.6)
A	KduI_1	e1ywkA2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: KduI_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	PF04962	KduI/IolB family (KduI)	KduI/IolB family	This family includes the 5-keto 4-deoxyuronate isomerase enzyme EC:5.3.1.17 that is involved in pectin degradation. This family aldo includes bacterial Myo-inositol catabolism (IolB) proteins. The Bacillus subtilis inositol operon (iolABCDEFGHIJ) is ...	This family includes the 5-keto 4-deoxyuronate isomerase enzyme EC:5.3.1.17 that is involved in pectin degradation. This family aldo includes bacterial Myo-inositol catabolism (IolB) proteins. The Bacillus subtilis inositol operon (iolABCDEFGHIJ) is involved in myo-inositol catabolism. Glucose repression of the iol operon induced by inositol is exerted through catabolite repression mediated by CcpA and the iol induction system mediated by IolR [2]. The exact function of IolB is unknown. Members of this family possess a Cupin like structure.	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	4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1	isomerase activity intramolecular oxidoreductase activity, interconverting aldoses and ketoses intramolecular oxidoreductase activity catalytic activity 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	catabolic process oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process monocarboxylic acid catabolic process D-glucuronate catabolic process glucuronate metabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process small molecule catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process monocarboxylic acid catabolic process D-glucuronate catabolic process glucuronate metabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process small molecule catabolic process glucuronate catabolic process monosaccharide metabolic process carbohydrate metabolic process D-galacturonate catabolic process carbohydrate catabolic process primary metabolic process D-galacturonate metabolic process monosaccharide catabolic process galacturonate catabolic process pectin metabolic process macromolecule catabolic process pectin catabolic process polysaccharide metabolic process polysaccharide catabolic process macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR027449	5-keto-4-deoxyuronate isomerase, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR011051	RmlC-like cupin domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR021120	KduI/IolB isomerase	Family
A, B, C, D, E A, B, C, D, E, F	IPR007045	5-keto 4-deoxyuronate isomerase	Family
A, B, C, D, E A, B, C, D, E, F	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.