1VGW

Crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritol 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	d1vgwa_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	Cytidylytransferase	4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)	(Neisseria gonorrhoeae ) [TaxId: 485 ],	SCOPe (2.08)
B	d1vgwb_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	Cytidylytransferase	4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)	(Neisseria gonorrhoeae ) [TaxId: 485 ],	SCOPe (2.08)
C	d1vgwc_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	Cytidylytransferase	4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)	(Neisseria gonorrhoeae ) [TaxId: 485 ],	SCOPe (2.08)
D	d1vgwd_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	Cytidylytransferase	4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)	(Neisseria gonorrhoeae ) [TaxId: 485 ],	SCOPe (2.08)
E	d1vgwe_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	Cytidylytransferase	4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)	(Neisseria gonorrhoeae ) [TaxId: 485 ],	SCOPe (2.08)
F	d1vgwf_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	Cytidylytransferase	4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)	(Neisseria gonorrhoeae ) [TaxId: 485 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8035736	3000077	SCOP2B (2022-06-29)
B	SCOP2 Family	Cytidylytransferase	8023356	4002789	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Nucleotide-diphospho-sugar transferases	8035736	3000077	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8035736	3000077	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8035736	3000077	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8035736	3000077	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8035736	3000077	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	IspD	e1vgwA1	A: a/b three-layered sandwiches	X: Nucleotide-diphospho-sugar transferases (From Topology)	H: Nucleotide-diphospho-sugar transferases (From Topology)	T: Nucleotide-diphospho-sugar transferases	F: IspD	ECOD (1.6)
B	IspD	e1vgwB1	A: a/b three-layered sandwiches	X: Nucleotide-diphospho-sugar transferases (From Topology)	H: Nucleotide-diphospho-sugar transferases (From Topology)	T: Nucleotide-diphospho-sugar transferases	F: IspD	ECOD (1.6)
C	IspD	e1vgwC1	A: a/b three-layered sandwiches	X: Nucleotide-diphospho-sugar transferases (From Topology)	H: Nucleotide-diphospho-sugar transferases (From Topology)	T: Nucleotide-diphospho-sugar transferases	F: IspD	ECOD (1.6)
D	IspD	e1vgwD1	A: a/b three-layered sandwiches	X: Nucleotide-diphospho-sugar transferases (From Topology)	H: Nucleotide-diphospho-sugar transferases (From Topology)	T: Nucleotide-diphospho-sugar transferases	F: IspD	ECOD (1.6)
E	IspD	e1vgwE1	A: a/b three-layered sandwiches	X: Nucleotide-diphospho-sugar transferases (From Topology)	H: Nucleotide-diphospho-sugar transferases (From Topology)	T: Nucleotide-diphospho-sugar transferases	F: IspD	ECOD (1.6)
F	IspD	e1vgwF1	A: a/b three-layered sandwiches	X: Nucleotide-diphospho-sugar transferases (From Topology)	H: Nucleotide-diphospho-sugar transferases (From Topology)	T: Nucleotide-diphospho-sugar transferases	F: IspD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
B	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
C	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
D	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
E	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
F	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	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	PF01128	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD)	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	-	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	4-diphosphocytidyl-2C-methyl-D-erythritol synthase	cytidylyltransferase activity 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR034683	Cytidylyltransferase IspD/TarI	Family
A, B, C, D, E A, B, C, D, E, F	IPR018294	4-diphosphocytidyl-2C-methyl-D-erythritol synthase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001228	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	Family
A, B, C, D, E A, B, C, D, E, F	IPR050088	IspD/TarI cytidylyltransferase, baterial-type	Family

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.