1W55

Structure of the Bifunctional IspDF from Campylobacter jejuni

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	d1w55a1	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	Cytidylytransferase	IspD/IspF bifunctional enzyme, CDP-me synthase domain	(Campylobacter jejuni ) [TaxId: 197 ],	SCOPe (2.08)
A	d1w55a2	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	IspD/ispF bifunctional enzyme, MECDP synthase domain	(Campylobacter jejuni ) [TaxId: 197 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Cytidylytransferase	8030891	4002789	SCOP2 (2022-06-29)
A	SCOP2 Family	IpsF-like	8030893	4003475	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleotide-diphospho-sugar transferases	8043270	3000077	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	IpsF-like	8043272	3000926	SCOP2 (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	e1w55A1	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)
A	IspD	e1w55A2	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)
A	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	PF01128	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD)	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	-	Family
A	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	ISPD/ISPF BIFUNCTIONAL ENZYME	phosphorus-oxygen lyase activity 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity lyase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding cytidylyltransferase activity 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity transferase activity nucleotidyltransferase 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 terpenoid biosynthetic process terpenoid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036571	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily	Homologous Superfamily
A	IPR026596	Bifunctional enzyme IspD/IspF	Family
A	IPR018294	4-diphosphocytidyl-2C-methyl-D-erythritol synthase, conserved site	Conserved Site
A	IPR003526	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	Domain
A	IPR020555	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, conserved site	Conserved Site
A	IPR001228	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	Family
A	IPR034683	Cytidylyltransferase IspD/TarI	Family
A	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily

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.