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	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	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.