1VGW | pdb_00001vgw

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)
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)
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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	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)
D	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8035736	3000077	SCOP2B (2022-06-29)
C	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)
A	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)
F	HGTP_anticodon	e1vgwF1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: HGTP_anticodon	ECOD (develop294)
E	HGTP_anticodon	e1vgwE1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: HGTP_anticodon	ECOD (develop294)
D	HGTP_anticodon	e1vgwD1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: HGTP_anticodon	ECOD (develop294)
C	HGTP_anticodon	e1vgwC1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: HGTP_anticodon	ECOD (develop294)
B	HGTP_anticodon	e1vgwB1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: HGTP_anticodon	ECOD (develop294)
A	HGTP_anticodon	e1vgwA1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: HGTP_anticodon	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	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)
D	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)
B	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
A	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.