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Human Metabolome Database Version 2.5

 

Showing metabocard for (R)-Mevalonic acid-5-pyrophosphate (HMDB01981)

Legend: metabolite field enzyme field

Version 2.5
Creation Date 2006-05-22 15:17:30
Update Date 2009-05-05 20:59:00
Accession Number HMDB01981
Secondary Accession Numbers Not Available
Common Name (R)-Mevalonic acid-5-pyrophosphate
Description (R)-Mevalonic acid-5-pyrophosphate (mevalonate 5-diphosphate) is a directly synthesized product of mevalonate phosphate that is essential for cell proliferation. (PMID 2211719). It is a substrate for mevalonate-5-diphosphate decarboxylase, the third enzyme involved in the biosynthesis of cholesterol from mevalonic acid. This enzyme catalyzes the reaction of mevalonate 5-diphosphate (MVADP) with ATP to produce isopentenyl diphosphate, ADP, CO2, and inorganic phosphate. The overall reaction involves an anti elimination of the tertiary hydroxyl and carboxyl groups. This metabolite participates both in the biosynthesis of cholesterol and fatty acid mechanism, through which interpathway regulation could take place between the cholesterol and FA cascades. (PMID 8769113 )
Synonyms
  1. 1,1,3,7-tetrahydroxy-7-methyl-2,4-Dioxa-1,3-diphosphanonan-9-oic acid 1,3-dioxide
  2. 5-Pyrophosphomevalonate
  3. 5-Pyrophosphomevalonic acid
  4. Mevalonic 5-pyrophosphate
  5. Mevalonic acid 5-diphosphate
  6. Mevalonic acid 5-pyrophosphate
  7. Mevalonic acid pyrophosphate
  8. MVADP
  9. Pyrophosphomevalonate
  10. Pyrophosphomevalonic acid
  11. R-Mevalonic acid-5-Pyrophosphate
  12. R-Mevalonic acid-5-Pyrophosphic acid
  13. Mevalonate 5-diphosphate
  14. 1,1,3,7-tetrahydroxy-7-methyl-2,4-Dioxa-1,3-diphosphanonan-9-oate
  15. 1,1,3,7-tetrahydroxy-7-methyl-2,4-Dioxa-1,3-diphosphanonan-9-oic acid
Chemical IUPAC Name (3R)-3-hydroxy-5-(hydroxy(phosphonooxy)phosphoryloxy)-3-methylpentanoic 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 Not Available
BioCyc ID Not Available
BiGG ID Not Available
Wikipedia Link 5-Pyrophosphomevalonate Link Image
NuGOwiki Link HMDB01981 Link Image
Metagene Link HMDB01981 Link Image
METLIN ID 6415 Link Image
PubChem Compound Not Available
PubChem Substance Not Available
ChEBI ID Not Available
CAS Registry Number 1492-08-6
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-/m0/s1
Synthesis Reference Bloch, Konrad; Chaykin, S.; Phillips, A. H.; De Waard, A. Mevalonic acid pyrophosphate and isopentylpyrophosphate. Journal of Biological Chemistry (1959), 234 2595-2604.
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] Calculated using ALOGPS
Material Safety Data Sheet (MSDS) Not Available
MOL File Show Link Image
SDF File Show Link Image
PDB File Show Link Image
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 Not Available
Biofluid Location Not Available
Tissue Location
Tissue References
Lymphocyte —
Concentrations (Normal) Not Available
Concentrations (Abnormal) Not Available
Associated Disorders Not Available
OMIM ID Not Available
Pathways Not Available
General References
  1. Ku EC: Regulation of fatty acid biosynthesis by intermediates of the cholesterol biosynthetic pathway. Biochem Biophys Res Commun. 1996 Aug 5;225(1):173-9. [PubMed Link Image]
  2. 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]
  3. 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 (diphospho)decarboxylase
  2. MDDase
  3. Mevalonate pyrophosphate decarboxylase
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 43404.1
Enzyme 1 Theoretical pI 7.25
Enzyme 1 GO Classification
Function
  • ATP binding
  • adenyl nucleotide binding
  • adenyl ribonucleotide binding
  • binding
  • carbon-carbon lyase activity
  • carboxy-lyase activity
  • catalytic activity
  • diphosphomevalonate decarboxylase activity
  • kinase activity
  • lyase activity
  • nucleoside binding
  • purine nucleoside binding
  • transferase activity
  • transferase activity, transferring phosphorus-containing groups
Process
  • cellular lipid metabolic process
  • cellular metabolic process
  • isoprenoid biosynthetic process
  • isoprenoid metabolic process
  • lipid metabolic process
  • metabolic process
  • phosphate metabolic process
  • phosphorus metabolic process
  • phosphorylation
  • primary metabolic process
Component
—
Enzyme 1 General Function Involved in ATP binding
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 [RN:R01121]
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • None
Enzyme 1 Transmembrane Regions
  • None
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 12652543 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID P53602 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name MVD1_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 BC000011 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 1
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]
  2. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 Oct;14(10B):2121-7. [PubMed Link Image]
  3. Hinson DD, Chambliss KL, Toth MJ, Tanaka RD, Gibson KM: Post-translational regulation of mevalonate kinase by intermediates of the cholesterol and nonsterol isoprene biosynthetic pathways. J Lipid Res. 1997 Nov;38(11):2216-23. [PubMed Link Image]
  4. Molina H, Horn DM, Tang N, Mathivanan S, Pandey A: Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2199-204. Epub 2007 Feb 7. [PubMed Link Image]
  5. Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP: A quantitative atlas of mitotic phosphorylation. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. Epub 2008 Jul 31. [PubMed Link Image]
  6. Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S: Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. Anal Chem. 2009 Jun 1;81(11):4493-501. [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
  2. hPMK
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 21994.7
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 metabolic process
  • cholesterol biosynthetic process
  • cholesterol metabolic process
  • metabolic process
  • small molecule metabolic process
  • sterol metabolic process
Component
  • cell part
  • cytoplasm
  • intracellular part
Enzyme 2 General Function Involved in phosphomevalonate kinase activity
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 [RN:R03245]
Enzyme 2 Pfam Domain Function
Enzyme 2 Signals
  • None
Enzyme 2 Transmembrane Regions
  • None
Enzyme 2 Essentiality Not Available
Enzyme 2 GenBank ID Protein Not Available
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 1q22
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. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 Oct;14(10B):2121-7. [PubMed Link Image]
  3. 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]
  4. Hinson DD, Chambliss KL, Toth MJ, Tanaka RD, Gibson KM: Post-translational regulation of mevalonate kinase by intermediates of the cholesterol and nonsterol isoprene biosynthetic pathways. J Lipid Res. 1997 Nov;38(11):2216-23. [PubMed Link Image]
  5. Herdendorf TJ, Miziorko HM: Phosphomevalonate kinase: functional investigation of the recombinant human enzyme. Biochemistry. 2006 Mar 14;45(10):3235-42. [PubMed Link Image]
  6. Herdendorf TJ, Miziorko HM: Functional evaluation of conserved basic residues in human phosphomevalonate kinase. Biochemistry. 2007 Oct 23;46(42):11780-8. Epub 2007 Sep 29. [PubMed Link Image]
  7. Chang Q, Yan XX, Gu SY, Liu JF, Liang DC: Crystal structure of human phosphomevalonate kinase at 1.8 A resolution. Proteins. 2008 Oct;73(1):254-8. [PubMed Link Image]
Enzyme 2 Metabolite References Not Available