5IWY | pdb_00005iwy

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis complexed with CMP and Mg2+

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	d5iwya_	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	d5iwyb_	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	d5iwyc_	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	d5iwyd_	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	d5iwye_	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	d5iwyf_	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	SCOP2B Superfamily	IpsF-like	8081210	3000926	SCOP2B (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	e5iwyA1	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	e5iwyB1	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	e5iwyC1	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	e5iwyD1	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	e5iwyE1	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	e5iwyF1	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	isoprenoid biosynthetic process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway isopentenyl diphosphate biosynthetic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process glyceraldehyde-3-phosphate metabolic process phospholipid biosynthetic process aldehyde metabolic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process isoprenoid biosynthetic process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway isopentenyl diphosphate biosynthetic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process glyceraldehyde-3-phosphate metabolic process phospholipid biosynthetic process aldehyde metabolic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic 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 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.