6XR5 | pdb_00006xr5

Crystal Structure of Diphosphomevalonate decarboxylase (MVD1) Cryptococcus neoformans var. grubii serotype A

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
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)
H	d6xr5h1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
H	d6xr5h2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	automated matches	automated matches	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
H	d6xr5h3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
G	d6xr5g1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
G	d6xr5g2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	automated matches	automated matches	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
F	d6xr5f1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
F	d6xr5f2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	automated matches	automated matches	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
E	d6xr5e1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
E	d6xr5e2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	automated matches	automated matches	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
D	d6xr5d1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
D	d6xr5d2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	automated matches	automated matches	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
D	d6xr5d3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
C	d6xr5c1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
C	d6xr5c2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	automated matches	automated matches	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
C	d6xr5c3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
B	d6xr5b1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
B	d6xr5b2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	automated matches	automated matches	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
B	d6xr5b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
A	d6xr5a1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
A	d6xr5a2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	automated matches	automated matches	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)
A	d6xr5a3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Cryptococcus neoformans H99 ) [TaxId: 235443 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	GHMP_kinases_N_1	e6xr5H2	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)
H	KOG2833	e6xr5H1	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)
G	GHMP_kinases_N_1	e6xr5G2	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)
G	KOG2833	e6xr5G1	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)
F	GHMP_kinases_N_1	e6xr5F1	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)
F	KOG2833	e6xr5F2	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)
E	GHMP_kinases_N_1	e6xr5E2	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)
E	KOG2833	e6xr5E1	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)
D	GHMP_kinases_N_1	e6xr5D2	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)
D	KOG2833	e6xr5D1	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)
C	GHMP_kinases_N_1	e6xr5C2	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)
C	KOG2833	e6xr5C1	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)
B	GHMP_kinases_N_1	e6xr5B2	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)
B	KOG2833	e6xr5B1	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)
A	GHMP_kinases_N_1	e6xr5A2	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	e6xr5A1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	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, B, C, D, E A, B, C, D, E, F, G, H	PF22700	Diphosphomevalonate decarboxylase-like N-terminal domain (MVD-like_N)	Diphosphomevalonate decarboxylase-like N-terminal domain	This entry represents the N-terminal domain of Diphosphomevalonate decarboxylases [1-5] whoch catalyse the ATP dependent decarboxylation of (R)-5-diphosphomevalonate to form isopentenyl diphosphate (IPP). Members of this entry function in the mevalon ...	This entry represents the N-terminal domain of Diphosphomevalonate decarboxylases [1-5] whoch catalyse the ATP dependent decarboxylation of (R)-5-diphosphomevalonate to form isopentenyl diphosphate (IPP). Members of this entry function in the mevalonate pathway leading to isopentenyl diphosphate (IPP), a key precursor for the biosynthesis of isoprenoids and sterol synthesis.	Domain

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, G, H	Diphosphomevalonate decarboxylase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide 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	sterol biosynthetic process biosynthetic process steroid metabolic process sterol metabolic process lipid biosynthetic process primary metabolic process metabolic process cellular process steroid biosynthetic process lipid metabolic process isopentenyl diphosphate biosynthetic process acetyl-CoA metabolic process phospholipid metabolic process nucleobase-containing compound metabolic process sterol biosynthetic process biosynthetic process steroid metabolic process sterol metabolic process lipid biosynthetic process primary metabolic process metabolic process cellular 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 small molecule metabolic process amide 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

InterPro: Protein Family Classification InterPro Database Homepage

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