4RKP | pdb_00004rkp

Crystal Structure of Mevalonate-3-Kinase from Thermoplasma acidophilum (apo form)

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	M3K_C, MVD-like_N	e4rkpB1	A: a/b three-layered sandwiches	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: M3K_C, MVD-like_N	ECOD (v294.1)
B	Lipocalin	e4rkpB2	A: a/b three-layered sandwiches	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: Lipocalin	ECOD (v294.1)
A	Peptidase_M99_C	e4rkpA1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Peptidase_M99_C	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21433	Mevalonate-3-kinase, C-terminal domain (M3K_C)	Mevalonate-3-kinase, C-terminal domain	Mevalonate-3-kinase (M3K) is a mevalonate diphosphate decarboxylase (MDD) homologue from Thermoplasma acidophilum, which catalyses phosphorylation of (R)-mevalonate without concomitant decarboxylation [1]. This entry represents the C-terminal domain ...	Mevalonate-3-kinase (M3K) is a mevalonate diphosphate decarboxylase (MDD) homologue from Thermoplasma acidophilum, which catalyses phosphorylation of (R)-mevalonate without concomitant decarboxylation [1]. This entry represents the C-terminal domain of M3K.	Domain
A, B	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	Putative uncharacterized protein Ta1305	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 kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups phosphotransferase activity, alcohol group as acceptor	isopentenyl diphosphate biosynthetic process lipid 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 phosphorus metabolic process nucleoside phosphate metabolic process isoprenoid biosynthetic process primary metabolic process isopentenyl diphosphate biosynthetic process lipid 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 phosphorus metabolic process nucleoside phosphate metabolic process isoprenoid biosynthetic process primary metabolic process phospholipid biosynthetic process purine-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process metabolic process cellular process isopentenyl diphosphate biosynthetic process, mevalonate pathway lipid metabolic process isoprenoid metabolic process isopentenyl diphosphate metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR053859	Diphosphomevalonate decarboxylase-like N-terminal domain	Domain
A, B	IPR048470	Mevalonate-3-kinase, C-terminal domain	Domain
A, B	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A, B	IPR048471	Mevalonate-3-kinase	Family
A, B	IPR036554	GHMP kinase, C-terminal domain superfamily	Homologous Superfamily
A, B	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.