2F2H | pdb_00002f2h

Structure of the YicI thiosugar Michaelis complex

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	d2f2hf2	All beta proteins	Supersandwich	Galactose mutarotase-like	Glycosyl hydrolase family 31, N-terminal domain-like	Putative glucosidase YicI, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2f2hf3	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Glycosyl hydrolase family 31, domain 3	Putative glucosidase YicI, domain 3	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2f2hf1	All beta proteins	Glycolsyl hydrolase family 31 C-terminal domain-like	Glycolsyl hydrolase family 31 C-terminal domain	Glycolsyl hydrolase family 31 C-terminal domain	Putative glucosidase YicI, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2f2hf4	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	Glycosyl hydrolase family 31 catalytic domain	Putative glucosidase YicI, domain 2	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2f2hf5	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2f2he2	All beta proteins	Supersandwich	Galactose mutarotase-like	Glycosyl hydrolase family 31, N-terminal domain-like	Putative glucosidase YicI, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2f2he3	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Glycosyl hydrolase family 31, domain 3	Putative glucosidase YicI, domain 3	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2f2he1	All beta proteins	Glycolsyl hydrolase family 31 C-terminal domain-like	Glycolsyl hydrolase family 31 C-terminal domain	Glycolsyl hydrolase family 31 C-terminal domain	Putative glucosidase YicI, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2f2he4	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	Glycosyl hydrolase family 31 catalytic domain	Putative glucosidase YicI, domain 2	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2f2he5	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2f2hd2	All beta proteins	Supersandwich	Galactose mutarotase-like	Glycosyl hydrolase family 31, N-terminal domain-like	Putative glucosidase YicI, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2f2hd3	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Glycosyl hydrolase family 31, domain 3	Putative glucosidase YicI, domain 3	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2f2hd1	All beta proteins	Glycolsyl hydrolase family 31 C-terminal domain-like	Glycolsyl hydrolase family 31 C-terminal domain	Glycolsyl hydrolase family 31 C-terminal domain	Putative glucosidase YicI, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2f2hd4	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	Glycosyl hydrolase family 31 catalytic domain	Putative glucosidase YicI, domain 2	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2f2hd5	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2f2hc2	All beta proteins	Supersandwich	Galactose mutarotase-like	Glycosyl hydrolase family 31, N-terminal domain-like	Putative glucosidase YicI, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2f2hc3	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Glycosyl hydrolase family 31, domain 3	Putative glucosidase YicI, domain 3	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2f2hc1	All beta proteins	Glycolsyl hydrolase family 31 C-terminal domain-like	Glycolsyl hydrolase family 31 C-terminal domain	Glycolsyl hydrolase family 31 C-terminal domain	Putative glucosidase YicI, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2f2hc4	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	Glycosyl hydrolase family 31 catalytic domain	Putative glucosidase YicI, domain 2	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2f2hc5	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2f2hb2	All beta proteins	Supersandwich	Galactose mutarotase-like	Glycosyl hydrolase family 31, N-terminal domain-like	Putative glucosidase YicI, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2f2hb3	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Glycosyl hydrolase family 31, domain 3	Putative glucosidase YicI, domain 3	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2f2hb1	All beta proteins	Glycolsyl hydrolase family 31 C-terminal domain-like	Glycolsyl hydrolase family 31 C-terminal domain	Glycolsyl hydrolase family 31 C-terminal domain	Putative glucosidase YicI, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2f2hb4	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	Glycosyl hydrolase family 31 catalytic domain	Putative glucosidase YicI, domain 2	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2f2hb5	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2f2ha2	All beta proteins	Supersandwich	Galactose mutarotase-like	Glycosyl hydrolase family 31, N-terminal domain-like	Putative glucosidase YicI, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2f2ha3	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Glycosyl hydrolase family 31, domain 3	Putative glucosidase YicI, domain 3	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2f2ha1	All beta proteins	Glycolsyl hydrolase family 31 C-terminal domain-like	Glycolsyl hydrolase family 31 C-terminal domain	Glycolsyl hydrolase family 31 C-terminal domain	Putative glucosidase YicI, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2f2ha4	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	Glycosyl hydrolase family 31 catalytic domain	Putative glucosidase YicI, domain 2	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2f2ha5	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Galactose mutarotase-like	8040490	3000035	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	YicI C-terminal domain-like	8040489	3000267	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8040491	3001528	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	(Trans)glycosidases	8040493	3000313	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Galactose mutarotase-like	8040490	3000035	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8040491	3001528	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	YicI C-terminal domain-like	8040489	3000267	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	(Trans)glycosidases	8040493	3000313	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	YicI C-terminal domain-like	8040489	3000267	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	(Trans)glycosidases	8040493	3000313	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Galactose mutarotase-like	8040490	3000035	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8040491	3001528	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	(Trans)glycosidases	8040493	3000313	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Galactose mutarotase-like	8040490	3000035	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8040491	3001528	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	YicI C-terminal domain-like	8040489	3000267	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Trans)glycosidases	8040493	3000313	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Galactose mutarotase-like	8040490	3000035	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8040491	3001528	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	YicI C-terminal domain-like	8040489	3000267	SCOP2B (2022-06-29)
A	SCOP2 Family	YicI C-terminal domain-like	8028110	4003108	SCOP2 (2022-06-29)
A	SCOP2 Family	YicI N-terminal domain-like	8028111	4003123	SCOP2 (2022-06-29)
A	SCOP2 Family	YicI post-catalytic domain-like	8028112	4003233	SCOP2 (2022-06-29)
A	SCOP2 Family	YicI catalytic domain-like	8028114	4003298	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	YicI C-terminal domain-like	8040489	3000267	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Galactose mutarotase-like	8040490	3000035	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glycosyl hydrolase domain-like	8040491	3001528	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	(Trans)glycosidases	8040493	3000313	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	Crystall	e2f2hF1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Crystall	ECOD (v294.1)
F	DUF711	e2f2hF4	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)
E	Crystall	e2f2hE1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Crystall	ECOD (v294.1)
E	DUF711	e2f2hE4	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)
D	Crystall	e2f2hD1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Crystall	ECOD (v294.1)
D	DUF711	e2f2hD4	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)
C	Crystall	e2f2hC1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Crystall	ECOD (v294.1)
C	DUF711	e2f2hC4	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)
B	Crystall	e2f2hB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Crystall	ECOD (v294.1)
B	DUF711	e2f2hB4	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)
A	Glyco_hydro_31_3rd	e2f2hA1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: Glyco_hydro_31_3rd	ECOD (v294.1)
A	Gal_mutarotas_2	e2f2hA2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich	T: supersandwich	F: Gal_mutarotas_2	ECOD (v294.1)
A	Glyco_hydro_31_2nd	e2f2hA4	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Glyco_hydro_31_2nd	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.60.40.1760	Mainly Beta	Sandwich	Immunoglobulin-like	glycosyl hydrolase (family 31)	CATH (4.3.0)
F	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
F	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)
E	2.60.40.1760	Mainly Beta	Sandwich	Immunoglobulin-like	glycosyl hydrolase (family 31)	CATH (4.3.0)
E	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
E	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)
D	2.60.40.1760	Mainly Beta	Sandwich	Immunoglobulin-like	glycosyl hydrolase (family 31)	CATH (4.3.0)
D	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
D	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)
C	2.60.40.1760	Mainly Beta	Sandwich	Immunoglobulin-like	glycosyl hydrolase (family 31)	CATH (4.3.0)
C	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
C	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)
B	2.60.40.1760	Mainly Beta	Sandwich	Immunoglobulin-like	glycosyl hydrolase (family 31)	CATH (4.3.0)
B	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
B	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)
A	2.60.40.1760	Mainly Beta	Sandwich	Immunoglobulin-like	glycosyl hydrolase (family 31)	CATH (4.3.0)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
A	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	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	PF21365	Glycosyl hydrolase family 31 C-terminal domain (Glyco_hydro_31_3rd)	Glycosyl hydrolase family 31 C-terminal domain	Glycosyl hydrolases are key enzymes of carbohydrate metabolism. Family 31 comprises of enzymes that are, or similar to, alpha- galactosidases. This entry represents the 3rd beta sandwich domain.	Domain
A, B, C, D, E A, B, C, D, E, F	PF13802	Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain (Gal_mutarotas_2)	Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain	This entry represents the first of three common domains found in Glycosyl hydrolase 31 family proteins. It has a galactose mutarotase superfamily fold.	Domain
A, B, C, D, E A, B, C, D, E, F	PF01055	Glycosyl hydrolases family 31 TIM-barrel domain (Glyco_hydro_31_2nd)	Glycosyl hydrolases family 31 TIM-barrel domain	Glycosyl hydrolases are key enzymes of carbohydrate metabolism. Family 31 comprises of enzymes that are, or similar to, alpha- galactosidases. This entry corresponds to the second domain of family 31 enzymes and adopts a TIM-barrel fold.	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	Putative family 31 glucosidase yicI	binding carbohydrate binding hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity alpha-D-xyloside xylohydrolase activity catalytic activity xyloglucan 1,6-alpha-xylosidase activity identical protein binding protein binding	carbohydrate metabolic process primary metabolic process metabolic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR000322	Glycoside hydrolase family 31, TIM barrel domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR050985	Alpha-glycosidase and related enzymes	Family
A, B, C, D, E A, B, C, D, E, F	IPR048395	Glycosyl hydrolase family 31, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR013780	Glycosyl hydrolase, all-beta	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR025887	Glycoside hydrolase family 31, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011013	Galactose mutarotase-like domain superfamily	Homologous Superfamily