5IWX

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	d5iwxa_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
B	d5iwxb_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
C	d5iwxc_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
D	d5iwxd_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
E	d5iwxe_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
F	d5iwxf_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	automated matches	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	IpsF-like	8081209	4003475	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	IpsF-like	8081210	3000926	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	IpsF-like	8081210	3000926	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	IpsF-like	8081210	3000926	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	IpsF-like	8081210	3000926	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	IpsF-like	8081210	3000926	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	IpsF-like	8081210	3000926	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	YgbB	e5iwxA1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF (From Topology)	T: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	F: YgbB	ECOD (1.6)
B	YgbB	e5iwxB1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF (From Topology)	T: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	F: YgbB	ECOD (1.6)
C	YgbB	e5iwxC1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF (From Topology)	T: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	F: YgbB	ECOD (1.6)
D	YgbB	e5iwxD1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF (From Topology)	T: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	F: YgbB	ECOD (1.6)
E	YgbB	e5iwxE1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF (From Topology)	T: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	F: YgbB	ECOD (1.6)
F	YgbB	e5iwxF1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF (From Topology)	T: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	F: YgbB	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF02542	YgbB family (YgbB)	YgbB family	-	Family

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	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	cation binding ion binding binding metal ion binding small molecule binding phosphorus-oxygen lyase activity 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity lyase activity catalytic activity	cellular biosynthetic process isopentenyl diphosphate biosynthetic process lipid biosynthetic process carbohydrate derivative metabolic process glyceraldehyde-3-phosphate metabolic process phospholipid metabolic process organic substance metabolic process cellular aldehyde metabolic process organic substance biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process isoprenoid biosynthetic process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway cellular metabolic process cellular biosynthetic process isopentenyl diphosphate biosynthetic process lipid biosynthetic process carbohydrate derivative metabolic process glyceraldehyde-3-phosphate metabolic process phospholipid metabolic process organic substance metabolic process cellular aldehyde metabolic process organic substance biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process isoprenoid biosynthetic process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway cellular metabolic process primary metabolic process phospholipid biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process cellular lipid metabolic process metabolic process cellular process lipid metabolic process isoprenoid metabolic process isopentenyl diphosphate metabolic process terpenoid biosynthetic process terpenoid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR036571	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR003526	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	Domain
A, B, C, D, E A, B, C, D, E, F	IPR020555	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, conserved site	Conserved Site

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.