1VH8

Crystal structure of a 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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)
A	d1vh8a1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
A	d1vh8a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
B	d1vh8b1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
B	d1vh8b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
D	d1vh8d1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
D	d1vh8d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
E	d1vh8e1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
E	d1vh8e2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
F	d1vh8f1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
F	d1vh8f2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
C	d1vh8c1	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
C	d1vh8c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Haemophilus influenzae ) [TaxId: 727 ],	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	8023407	4003475	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	IpsF-like	8035787	3000926	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	IpsF-like	8035787	3000926	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	IpsF-like	8035787	3000926	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	IpsF-like	8035787	3000926	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	IpsF-like	8035787	3000926	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	IpsF-like	8035787	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	e1vh8A1	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	e1vh8B1	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	e1vh8D1	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	e1vh8E1	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	e1vh8F1	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	e1vh8C1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
B	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
D	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
E	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
F	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
C	3.30.1330.50	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	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	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 cellular aldehyde metabolic 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 cellular biosynthetic process isopentenyl diphosphate biosynthetic process lipid biosynthetic process carbohydrate derivative metabolic process glyceraldehyde-3-phosphate metabolic process phospholipid metabolic process cellular aldehyde metabolic 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 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.