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Human Metabolome Database Version 2.5

 

Showing metabocard for 5-Diphosphomevalonic acid (HMDB01090)

Legend: metabolite field enzyme field

Version 2.5
Creation Date 2005-11-16 15:48:42
Update Date 2009-05-05 20:58:29
Accession Number HMDB01090
Secondary Accession Numbers Not Available
Common Name 5-Diphosphomevalonic acid
Description 5-pyrophosphomevalonate is a metabolic intermediate in the mevalonate pathway, catalyzed by the enzyme phosphomevalonate kinase from 5-phosphomevalonate. (wikipedia)
Synonyms
  1. (R)-5-Diphosphomevalonate
  2. 1,1,3,7-tetrahydroxy-7-methyl-2,4-dioxa-1,3-diphosphanonan-9-oic acid ion(1-)1,3-dioxide
  3. 5-diphosphomevalonate
  4. 5-diphosphomevalonic acid
  5. mevalonate 5-diphosphate
  6. mevalonate pyrophosphate
  7. mevalonate-diphosphate
  8. 1,1,3,7-tetrahydroxy-7-methyl-2,4-dioxa-1,3-diphosphanonan-9-oate
  9. 1,1,3,7-tetrahydroxy-7-methyl-2,4-dioxa-1,3-diphosphanonan-9-oic acid
Chemical IUPAC Name 3-hydroxy-5-(hydroxy-phosphonooxy-phosphoryl)oxy-3-methyl-pentanoic acid
Chemical Formula C6H14O10P2
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Miscellaneous
Class
  • Acyl Phosphates
Sub Class
  • Short chain acyl phosphates
Family
  • Mammalian Metabolite
Species
  • tertiary alcohol
  • carboxylic acid
  • phosphoric acid ester
Biofunction
—
Application
—
Source
  • Endogenous
Average Molecular Weight 308.117
Monoisotopic Molecular Weight 308.006226
Isomeric SMILES C[C@@](O)(CCOP(O)(=O)OP(O)(O)=O)CC(O)=O
Canonical SMILES CC(O)(CCOP(O)(=O)OP(O)(O)=O)CC(O)=O
KEGG Compound ID C01143 Link Image
BioCyc ID CPD-641 Link Image
BiGG ID 36910 Link Image
Wikipedia Link 5-Diphosphomevalonic acid Link Image
NuGOwiki Link HMDB01090 Link Image
Metagene Link HMDB01090 Link Image
METLIN ID 5997 Link Image
PubChem Compound 516 Link Image
PubChem Substance 2467 Link Image
ChEBI ID 15899 Link Image
CAS Registry Number Not Available
InChI Identifier InChI=1/C6H14O10P2/c1-6(9,4-5(7)8)2-3-15-18(13,14)16-17(10,11)12/h9H,2-4H2,1H3,(H,7,8)(H,13,14)(H2,10,11,12)/t6-/m1/s1
Synthesis Reference Not Available
Melting Point (Experimental) Not Available
Experimental Water Solubility Not Available Source: PhysProp
Predicted Water Solubility 8.26 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge -4
State Solid
Experimental LogP/Hydrophobicity Not Available Source: PhysProp
Predicted LogP/Hydrophobicity -1.17 [Predicted by ALOGPS]; -3.3 [Predicted by PubChem via XLOGP] Calculated using ALOGPS
Material Safety Data Sheet (MSDS) Not Available
MOL File Show
SDF File Show
PDB File Show
2D Structure
3D Structure
Experimental PDB ID Not Available
Experimental 1H NMR Spectrum Not Available
Experimental 13C NMR Spectrum Not Available
Experimental 13C HSQC Spectrum Not Available
Predicted 1H NMR Spectrum Show Image
Show Peaklist
Predicted 13C NMR Spectrum Show Image
Show Peaklist
Mass Spectrum Not Available
Simplified TOCSY Spectrum Not Available
BMRB Spectrum Not Available
Cellular Location
  • peroxisome
Biofluid Location Not Available
Tissue Location Not Available
Concentrations (Normal) Not Available
Concentrations (Abnormal) Not Available
Associated Disorders Not Available
OMIM ID Not Available
Pathways
Name SMPDB Link KEGG Link
Steroid Biosynthesis SMP00023 Link Image map00100 Link Image
General References
  1. |
  2. Ma D, Nutt CL, Shanehsaz P, Peng X, Louis DN, Kaetzel DM: Autocrine platelet-derived growth factor-dependent gene expression in glioblastoma cells is mediated largely by activation of the transcription factor sterol regulatory element binding protein and is associated with altered genotype and patient survival in human brain tumors. Cancer Res. 2005 Jul 1;65(13):5523-34. [PubMed Link Image]
  3. Mitchell ED Jr, Avigan J: Control of phosphorylation and decarboxylation of mevalonic acid and its metabolites in cultured human fibroblasts and in rat liver in vivo. J Biol Chem. 1981 Jun 25;256(12):6170-3. [PubMed Link Image]
  4. Singh I, Pahan K, Khan M: Lovastatin and sodium phenylacetate normalize the levels of very long chain fatty acids in skin fibroblasts of X- adrenoleukodystrophy. FEBS Lett. 1998 Apr 24;426(3):342-6. [PubMed Link Image]
  5. Wadhwa R, Yaguchi T, Hasan MK, Taira K, Kaul SC: Mortalin-MPD (mevalonate pyrophosphate decarboxylase) interactions and their role in control of cellular proliferation. Biochem Biophys Res Commun. 2003 Mar 21;302(4):735-42. [PubMed Link Image]
  6. Toth MJ, Huwyler L: Molecular cloning and expression of the cDNAs encoding human and yeast mevalonate pyrophosphate decarboxylase. J Biol Chem. 1996 Apr 5;271(14):7895-8. [PubMed Link Image]
  7. Cuthbert JA, Lipsky PE: Inhibition by 6-fluoromevalonate demonstrates that mevalonate or one of the mevalonate phosphates is necessary for lymphocyte proliferation. J Biol Chem. 1990 Oct 25;265(30):18568-75. [PubMed Link Image]
  8. Hogenboom S, Tuyp JJ, Espeel M, Koster J, Wanders RJ, Waterham HR: Human mevalonate pyrophosphate decarboxylase is localized in the cytosol. Mol Genet Metab. 2004 Mar;81(3):216-24. [PubMed Link Image]
  9. Andreassi JL 2nd, Dabovic K, Leyh TS: Streptococcus pneumoniae isoprenoid biosynthesis is downregulated by diphosphomevalonate: an antimicrobial target. Biochemistry. 2004 Dec 28;43(51):16461-6. [PubMed Link Image]
  10. Zhou T, Daugherty M, Grishin NV, Osterman AL, Zhang H: Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily. Structure. 2000 Dec 15;8(12):1247-57. [PubMed Link Image]
  11. Hogenboom S, Wanders RJ, Waterham HR: Cholesterol biosynthesis is not defective in peroxisome biogenesis defective fibroblasts. Mol Genet Metab. 2003 Nov;80(3):290-5. [PubMed Link Image]
  12. Cuthbert JA, Lipsky PE: Negative regulation of cell proliferation by mevalonate or one of the mevalonate phosphates. J Biol Chem. 1991 Sep 25;266(27):17966-71. [PubMed Link Image]
  13. Wikipedia Link Image
Metabolic Enzymes
  1. Diphosphomevalonate decarboxylase
  2. Phosphomevalonate kinase
Enzyme 1 [top]
Enzyme 1 ID 6304
Enzyme 1 Name Diphosphomevalonate decarboxylase
Enzyme 1 Synonyms
  1. Mevalonate pyrophosphate decarboxylase
  2. Mevalonate
  3. diphosphodecarboxylase
Enzyme 1 Gene Name MVD
Enzyme 1 Protein Sequence >Diphosphomevalonate decarboxylase 
MASEKPLAAVTCTAPVNIAVIKYWGKRDEELVLPINSSLSVTLHQDQLKTTTTAVISKDF
TEDRIWLNGREEDVGQPRLQACLREIRCLARKRRNSRDGDPLPSSLSCKVHVASVNNFPT
AAGLASSAAGYACLAYTLARVYGVESDLSEVARRGSGSACRSLYGGFVEWQMGEQADGKD
SIARQVAPESHWPELRVLILVVSAEKKLTGSTVGMRASVETSPLLRFRAESVVPARMAEM
ARCIRERDFPSFAQLTMKDSNQFHATCLDTFPPISYLNAISWRIIHLVHRFNAHHGDTKV
AYTFDAGPNAVIFTLDDTVAEFVAAVWHGFPPGSNGDTFLKGLQVRPAPLSAELQAALAM
EPTPGGVKYIIVTQVGPGPQILDDPCAHLLGPDGLPKPAA
Enzyme 1 Number of Residues 400
Enzyme 1 Molecular Weight 43405
Enzyme 1 Theoretical pI 7.25
Enzyme 1 GO Classification
Function
  • ATP binding
  • adenyl nucleotide binding
  • binding
  • carbon-carbon lyase activity
  • carboxy-lyase activity
  • catalytic activity
  • diphosphomevalonate decarboxylase activity
  • kinase activity
  • lyase activity
  • nucleotide binding
  • purine nucleotide binding
  • transferase activity
  • transferase activity, transferring phosphorus-containing groups
Process
  • cellular lipid metabolism
  • cellular metabolism
  • isoprenoid biosynthesis
  • isoprenoid metabolism
  • lipid metabolism
  • metabolism
  • phosphate metabolism
  • phosphorus metabolism
  • phosphorylation
  • physiological process
  • primary metabolism
Component
—
Enzyme 1 General Function Lipid transport and metabolism
Enzyme 1 Specific Function Performs the first committed step in the biosynthesis of isoprenes
Enzyme 1 Pathways
Enzyme 1 Reactions
  • ATP + (R)-5-diphosphomevalonate = ADP + phosphate + isopentenyl diphosphate + CO2
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • None
Enzyme 1 Transmembrane Regions
  • None
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 1235682 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID P53602 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name ERG19_HUMAN Link Image
Enzyme 1 PDB ID Not Available
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >1203 bp 
ATGGCCTCGGAGAAGCCGCTGGCGGCAGTCACTTGTACAGCGCCGGTCAACATCGCGGTC
ATCAAGTACTGGGGCAAGCGCGATGAAGAGCTGGTTCTGCCCATCAACTCCTCCCTGAGC
GTCACTCTGCACCAGGACCAGTTAAAAACCACCACAACAGCCGTCATCAGCAAGGACTTC
ACCGAGGACCGGATTTGGCTGAATGGCCGGGAGGAGGATGTGGGGCAGCCGAGGCTGCAG
GCCTGCCTGCGGGAGATCCGCTGCCTGGCCCGGAAGCGGAGGAACTCACGGGATGGGGAC
CCGCTGCCCTCCAGCCTCAGCTGCAAGGTGCACGTGGCATCGGTGAACAACTTCCCCACG
GCTGCGGGCCTGGCCTCCTCAGCGGCGGGCTATGCCTGCCTAGCCTACACCCTGGCCCGT
GTCTACGGCGTGGAGAGTGACCTCTCAGAAGTGGCTCGCCGGGGCTCAGGCAGCGCCTGC
CGGAGCCTGTATGGGGGCTTTGTGGAGTGGCAGATGGGAGAGCAGGCCGACGGGAAGGAC
AGCATCGCTCGGCAAGTGGCCCCCGAGTCACACTGGCCTGAACTCCGCGTGCTCATCCTT
GTGGTGAGCGCTGAGAAGAAGCTGACAGGCAGTACCGTGGGCATGCGGGCCAGTGTGGAG
ACCAGCCCCCTGCTTCGGTTCCGGGCCGAGTCCGTGGTGCCCGCGCGCATGGCGGAGATG
GCCCGCTGCATCCGGGAGCGAGACTTCCCCAGCTTCGCCCAGCTGACCATGAAGGACAGC
AACCAGTTCCACGCCACCTGCCTCGACACCTTCCCGCCCATCTCTTACCTCAATGCCATC
TCCTGGCGCATCATCCACCTGGTGCACCGCTTCAACGCCCACCACGGGGACACCAAGGTG
GCGTACACCTTTGACGCGGGCCCCAATGCCGTGATCTTCACCCTGGACGACACTGTGGCT
GAGTTTGTGGCTGCTGTGTGGCACGGCTTTCCCCCAGGCTCGAATGGAGACACGTTTCTG
AAGGGGCTGCAGGTGAGGCCGGCCCCTCTCTCAGCTGAGCTTCAGGCTGCGCTGGCCATG
GAGCCGACCCCCGGTGGGGTCAAATACATCATTGTCACTCAGGTGGGGCCAGGGCCTCAA
ATCCTGGATGACCCCTGCGCCCACCTCCTGGGTCCTGACGGCCTGCCGAAGCCAGCTGCC
TGA
Enzyme 1 GenBank Gene ID U49260 Link Image
Enzyme 1 GeneCard ID MVD Link Image
Enzyme 1 GenAtlas ID MVD Link Image
Enzyme 1 HGNC ID HGNC:7529 Link Image
Enzyme 1 Chromosome Location 16
Enzyme 1 Locus 16q24.3
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References
  1. Toth MJ, Huwyler L: Molecular cloning and expression of the cDNAs encoding human and yeast mevalonate pyrophosphate decarboxylase. J Biol Chem. 1996 Apr 5;271(14):7895-8. [PubMed Link Image]
Enzyme 1 Metabolite References Not Available
Enzyme 2 [top]
Enzyme 2 ID 6305
Enzyme 2 Name Phosphomevalonate kinase
Enzyme 2 Synonyms
  1. PMKase
Enzyme 2 Gene Name PMVK
Enzyme 2 Protein Sequence >Phosphomevalonate kinase 
MAPLGGAPRLVLLFSGKRKSGKDFVTEALQSRLGADVCAVLRLSGPLKEQYAQEHGLNFQ
RLLDTSTYKEAFRKDMIRWGEEKRQADPGFFCRKIVEGISQPIWLVSDTRRVSDIQWFRE
AYGAVTQTVRVVALEQSRQQRGWVFTPGVDDAESECGLDNFGDFDWVIENHGVEQRLEEQ
LENLIEFIRSRL
Enzyme 2 Number of Residues 192
Enzyme 2 Molecular Weight 21995
Enzyme 2 Theoretical pI 5.41
Enzyme 2 GO Classification
Function
  • catalytic activity
  • kinase activity
  • phosphomevalonate kinase activity
  • transferase activity
  • transferase activity, transferring phosphorus-containing groups
Process
  • alcohol metabolism
  • cellular metabolism
  • cholesterol biosynthesis
  • cholesterol metabolism
  • metabolism
  • physiological process
  • sterol metabolism
Component
  • cell
  • cytoplasm
  • intracellular
Enzyme 2 General Function Not Available
Enzyme 2 Specific Function ATP + (R)-5-phosphomevalonate = ADP + (R)-5- diphosphomevalonate
Enzyme 2 Pathways
Enzyme 2 Reactions
  • ATP + (R)-5-phosphomevalonate = ADP + (R)-5-diphosphomevalonate
Enzyme 2 Pfam Domain Function
Enzyme 2 Signals
  • 1-21
Enzyme 2 Transmembrane Regions Not Available
Enzyme 2 Essentiality Not Available
Enzyme 2 GenBank ID Protein 1294782 Link Image
Enzyme 2 UniProtKB/Swiss-Prot ID Q15126 Link Image
Enzyme 2 UniProtKB/Swiss-Prot Entry Name PMVK_HUMAN Link Image
Enzyme 2 PDB ID Not Available
Enzyme 2 Cellular Location Not Available
Enzyme 2 Gene Sequence >579 bp 
ATGGCCCCGCTGGGAGGCGCCCCGCGGCTGGTACTGCTGTTCAGCGGCAAGAGGAAATCC
GGGAAGGACTTCGTGACCGAGGCGCTGCAGAGCAGACTTGGAGCTGATGTCTGTGCTGTC
CTCCGGCTCTCTGGTCCACTCAAGGAACAGTATGCTCAGGAGCATGGCTTGAACTTCCAG
AGACTCCTGGACACCAGCACCTACAAGGAGGCCTTTCGGAAGGACATGATCCGCTGGGGA
GAGGAGAAACGCCAGGCTGACCCAGGCTTCTTTTGCAGGAAGATTGTGGAGGGCATCTCC
CAGCCCATCTGGCTGGTGAGTGACACACGGAGAGTGTCTGACATCCAGTGGTTTCGGGAG
GCCTATGGGGCCGTGACGCAGACGGTCCGCGTTGTAGCGTTGGAGCAGAGCCGACAGCAG
CGGGGCTGGGTGTTCACGCCAGGGGTGGACGATGCTGAGTCAGAATGTGGCCTGGACAAC
TTCGGGGACTTTGACTGGGTCATCGAGAACCATGGAGTTGAACAGCGCCTGGAGGAGCAG
TTGGAGAACCTGATAGAATTTATCCGCTCCAGACTTTAG
Enzyme 2 GenBank Gene ID L77213 Link Image
Enzyme 2 GeneCard ID PMVK Link Image
Enzyme 2 GenAtlas ID PMVK Link Image
Enzyme 2 HGNC ID HGNC:9141 Link Image
Enzyme 2 Chromosome Location 1
Enzyme 2 Locus 1p13-q23
Enzyme 2 SNPs SNPJam Report Link Image
Enzyme 2 General References
  1. Chambliss KL, Slaughter CA, Schreiner R, Hoffmann GF, Gibson KM: Molecular cloning of human phosphomevalonate kinase and identification of a consensus peroxisomal targeting sequence. J Biol Chem. 1996 Jul 19;271(29):17330-4. [PubMed Link Image]
  2. Olivier LM, Chambliss KL, Gibson KM, Krisans SK: Characterization of phosphomevalonate kinase: chromosomal localization, regulation, and subcellular targeting. J Lipid Res. 1999 Apr;40(4):672-9. [PubMed Link Image]
Enzyme 2 Metabolite References Not Available