2PMP | pdb_00002pmp

Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from the isoprenoid biosynthetic pathway of Arabidopsis thaliana

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	d2pmpa_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	IpsF-like	IpsF-like	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	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	8081219	4003475	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	IpsF-like	8081220	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	Hydrolase	e2pmpA1	A: alpha bundles	X: Profilin-like	H: sensor domains	T: sensor domains	F: Hydrolase	ECOD (develop294)

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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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	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	pigment metabolic process carotenoid biosynthetic process isoprenoid biosynthetic process lipid biosynthetic process pigment biosynthetic process primary metabolic process terpenoid biosynthetic process biosynthetic process tetraterpenoid biosynthetic process metabolic process cellular process terpenoid metabolic process carotenoid metabolic process lipid metabolic process pigment metabolic process carotenoid biosynthetic process isoprenoid biosynthetic process lipid biosynthetic process pigment biosynthetic process primary metabolic process terpenoid biosynthetic process biosynthetic process tetraterpenoid biosynthetic process metabolic process cellular process terpenoid metabolic process carotenoid metabolic process lipid metabolic process isoprenoid metabolic process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway isopentenyl diphosphate biosynthetic process carbohydrate derivative metabolic process glyceraldehyde-3-phosphate metabolic process phospholipid biosynthetic process aldehyde metabolic process phospholipid metabolic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process isopentenyl diphosphate metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process chlorophyll metabolic process tetrapyrrole biosynthetic process porphyrin-containing compound metabolic process chlorophyll biosynthetic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast plastid stroma chloroplast stroma

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	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

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.