1FI4

THE X-RAY CRYSTAL STRUCTURE OF MEVALONATE 5-DIPHOSPHATE DECARBOXYLASE AT 2.3 ANGSTROM RESOLUTION.

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	d1fi4a1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	GHMP Kinase, N-terminal domain	Mevalonate 5-diphosphate decarboxylase	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1fi4a2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	Mevalonate 5-diphosphate decarboxylase	Mevalonate 5-diphosphate decarboxylase	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	GHMP Kinase, N-terminal domain	8020697	4000959	SCOP2 (2022-06-29)
A	SCOP2 Family	Mevalonate 5-diphosphate decarboxylase	8020698	4003543	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribosomal protein S5 domain 2-like	8033077	3000100	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GHMP Kinase, C-terminal domain	8033078	3001245	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	GHMP_kinases_N_1	e1fi4A2	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: GHMP_kinases_N_1	ECOD (1.6)
A	KOG2833	e1fi4A1	A: a+b two layers	X: Alpha-beta plaits	H: GHMP Kinase, C-terminal domain (From Topology)	T: GHMP Kinase, C-terminal domain	F: KOG2833	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
A	3.30.70.890	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	GHMP kinase, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18376	Mevalonate 5-diphosphate decarboxylase C-terminal domain (MDD_C)	Mevalonate 5-diphosphate decarboxylase C-terminal domain	Mevalonate diphosphate decarboxylase (EC:4.1.1.33) catalyzes the ATP dependent decarboxylation of mevalonate 5-diphosphate (MVAPP) to form isopentenyl 5-diphosphate. The reaction is required for production of polyisoprenoids and sterols from acetyl-C ...	Mevalonate diphosphate decarboxylase (EC:4.1.1.33) catalyzes the ATP dependent decarboxylation of mevalonate 5-diphosphate (MVAPP) to form isopentenyl 5-diphosphate. The reaction is required for production of polyisoprenoids and sterols from acetyl-CoA. This entry represents the C-terminal domain of the mevalonate 5-diphosphate decarboxylase enzyme which is a member of the GHMP kinase superfamily.	Domain
A	PF00288	GHMP kinases N terminal domain (GHMP_kinases_N)	GHMP kinases N terminal domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	MEVALONATE 5-DIPHOSPHATE DECARBOXYLASE	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding diphosphomevalonate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	phytosteroid metabolic process secondary alcohol biosynthetic process small molecule biosynthetic process organic hydroxy compound metabolic process steroid metabolic process sterol metabolic process lipid biosynthetic process primary metabolic process alcohol metabolic process ergosterol biosynthetic process phytosteroid biosynthetic process secondary alcohol metabolic process biosynthetic process sterol biosynthetic process organic hydroxy compound biosynthetic process phytosteroid metabolic process secondary alcohol biosynthetic process small molecule biosynthetic process organic hydroxy compound metabolic process steroid metabolic process sterol metabolic process lipid biosynthetic process primary metabolic process alcohol metabolic process ergosterol biosynthetic process phytosteroid biosynthetic process secondary alcohol metabolic process biosynthetic process sterol biosynthetic process organic hydroxy compound biosynthetic process alcohol biosynthetic process metabolic process cellular process small molecule metabolic process ergosterol metabolic process steroid biosynthetic process lipid metabolic process isopentenyl diphosphate biosynthetic process acetyl-CoA metabolic process phospholipid metabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process amide metabolic process thioester metabolic process phosphorus metabolic process nucleoside phosphate metabolic process isoprenoid biosynthetic process phospholipid biosynthetic process purine-containing compound metabolic process organophosphate metabolic process organophosphate biosynthetic process isopentenyl diphosphate biosynthetic process, mevalonate pathway isoprenoid metabolic process isopentenyl diphosphate metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle vacuole intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR053859	Diphosphomevalonate decarboxylase-like N-terminal domain	Domain
A	IPR036554	GHMP kinase, C-terminal domain superfamily	Homologous Superfamily
A	IPR029765	Diphosphomevalonate decarboxylase	Family
A	IPR005935	Diphosphomevalonate/phosphomevalonate decarboxylase	Family
A	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A	IPR041431	Mvd1, C-terminal	Domain
A	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	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.