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Bovine Rumen Metabolome Database



Showing metabocard for D-Ribose (RMDB00283)

Legend: metabolite field enzyme field

Version 1.0
Creation Date 2005-11-16 15:48:42
Update Date 2009-05-05 20:57:49
Accession Number RMDB00283
Common Name D-Ribose
Description D-ribose is commonly referred to simply as ribose, a five-carbon sugar found in all living cells. Ribose is not an essential nutrient because it can be synthesized by almost every tissue in the body from other substances, such as glucose. It is vital for life as a component of DNA, RNA, ATP, ADP, and AMP. In nature, small amounts of ribose can be found in ripe fruits and vegetables. Brewer's yeast, which has a high concentration of RNA, is another rich source of ribose. D-ribose is also a component of many so-called energy drinks and antiaging products available on the market today. Ribose is a structural component of ATP, which is the primary energy source for exercising muscle. The adenosine component is an adenine base attached to the five-carbon sugar ribose. ATP provides energy to working muscles by releasing a phosphate group, hence becoming ADP, which in turn may release a phosphate group, then becoming AMP. During intense muscular activity, the total amount of ATP available is quickly depleted. In an effort to correct this imbalance, AMP is broken down in the muscle and secreted from the cell. Once the breakdown products of AMP are released from the cell, the energy potential (TAN pool) of the muscle is reduced and ATP must then be reformed using ribose. Ribose helps restore the level of adenine nucleotides by bypassing the rate-limiting step in the de novo (oxidative pentose phosphate) pathway, which regenerates 5-phosphoribosyl-l-pyrophosphate (PRPP), the essential precursor for ATP. If ribose is not readily available to a cell, glucose may be converted to ribose. Ribose supplementation has been shown to increase the rate of ATP resynthesis following intense exercise. The use of ribose in men with severe coronary artery disease resulted in improved exercise tolerance. Hence, there is interest in the potential of ribose supplements to boost muscular performance in athletic activities. (PMID: 17618002, Curr Sports Med Rep. 2007 Jul;6(4):254-7.)
Synonyms
  1. d-Ribose
  2. Alpha-d-ribose
  3. D-Ribo-2,3,4,5-tetrahydroxyvaleraldehyde
  4. D-(-)-ribose
  5. Ribose
  6. alpha-D-ribose-5
  7. delta-Ribose
  8. Alpha-delta-ribose
  9. delta-Ribo-2,3,4,5-tetrahydroxyvaleraldehyde
  10. delta-(-)-ribose
  11. alpha-delta-ribose-5
Chemical IUPAC Name (3R,4R,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol
Chemical Formula C5H10O5
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Carbohydrates and Carbohydrate conjugates
Class
  • Carbohydrates
Sub Class
  • Monosaccharides
Family
  • Mammalian_Metabolite
Species
  • hemiacetal; primary alcohol; secondary alcohol; 1,2-diol; heterocyclic compound
Biofunction
  • Second messenger
Application
Source
  • Endogenous
Average Molecular Weight 150.130
Monoisotopic Molecular Weight 150.052826
Isomeric SMILES OC[C@H]1OC(O)[C@H](O)[C@@H]1O
Canonical SMILES OCC1OC(O)C(O)C1O
KEGG Compound ID C00121 Link Image
BioCyc ID CPD-560 Link Image
BiGG ID 33936 Link Image
Wikipedia Link Ribose Link Image
METLIN ID 313 Link Image
PubChem Compound 5779 Link Image
PubChem Substance 3421 Link Image
ChEBI ID 16988 Link Image
CAS Registry Number 50-69-1
InChI Identifier InChI=1/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5?/m1/s1
Synthesis Reference Park, Yong-Cheol; Choi, Jin-Ho; Bennett, George N.; Seo, Jin-Ho. Characterization of D-ribose biosynthesis in Bacillus subtilis JY200 deficient in transketolase gene. Journal of Biotechnology (2006), 121(4), 508-516.
Melting Point (Experimental) 95 oC
Experimental Water Solubility Not Available Source: PhysProp
Predicted Water Solubility 1000.0 mg/mL [MEYLAN,WM et al. (1996)]; 1.07e+03 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge 0
State Solid
Experimental LogP/Hydrophobicity -2.32 [HANSCH,C ET AL. (1995)] Source: PhysProp
Predicted LogP/Hydrophobicity -2.65 [Predicted by ALOGPS]; -1.9 [Predicted by PubChem via XLOGP] Calculated using ALOGPS
Material Safety Data Sheet (MSDS)
MOL File Show Link Image
SDF File Show Link Image
PDB File Show Link Image
2D Structure
3D Structure
Experimental PDB ID 1GQT Link Image
Experimental PDB File Show
Experimental PDB Structure
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
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Mass Spectrum
Low Energy
Download File
Show Experimental Conditions Link Image
Medium Energy
Download File
Show Experimental Conditions Link Image
High Energy
Download File
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Simplified TOCSY Spectrum Not Available
BMRB Spectrum Not Available
Cellular Location
  • Cytoplasm (Predicted from LogP)
  • Extracellular
Biofluid Location
  • Rumen
Tissue Location
Concentrations (Normal)
Biofluid Rumen
Value 311.38 +/- 39.97 uM
Age 4-5 years old
Sex Female (lactating)
Condition Normal (0% barley grain in dry matter (DM) basis)
Breed Holstein-Friesian
Experimental Condition Rumen fluid for the analysis was collected 15-20 minutes before the morning feeding on days 12 and 21 of each experimental period. Cows were fed once daily at 0800.
Comments Not Available
References
  • The rumen metabolome (in preparation)
Biofluid Rumen
Value 237.5 +/- 0.7 uM
Age N/A
Sex Female
Condition Normal
Breed Not Available
Experimental Condition Not Available
Comments Not Available
References
  • Metabolomics reveals unhealthy alterations in rumen metabolism with increased proportion of cereal grain in the diet of dairy cows. Burim N. Ametaj, Qendrim Zebeli, Fozia Saleem, Nikolaos Psychogios, Michael J. Lewis, Suzanna M. Dunn, Jianguo Xia and David S. Wishart Metabolomics 2010;6(4):583-594
Concentrations (Abnormal)
Biofluid Rumen
Value 323 +/- 70 uM
Age 4-5 years old
Sex Female (lactating)
Condition 15% barley grain in dry matter (DM) basis
Breed Holstein-Friesian
Experimental Condition Rumen fluid for the analysis was collected 15-20 minutes before the morning feeding on days 12 and 21 of each experimental period. Cows were fed once daily at 0800.
Comments Not Available
References
  • The rumen metabolome (in preparation)
Biofluid Rumen
Value 406 +/- 95 uM
Age 4-5 years old
Sex Female (lactating)
Condition 30% barley grain in dry matter (DM) basis
Breed Holstein-Friesian
Experimental Condition Rumen fluid for the analysis was collected 15-20 minutes before the morning feeding on days 12 and 21 of each experimental period. Cows were fed once daily at 0800.
Comments Not Available
References
  • The rumen metabolome (in preparation)
Biofluid Rumen
Value 255 +/- 78 uM
Age 4-5 years old
Sex Female (lactating)
Condition 45% barley grain in dry matter (DM) basis
Breed Holstein-Friesian
Experimental Condition Rumen fluid for the analysis was collected 15-20 minutes before the morning feeding on days 12 and 21 of each experimental period. Cows were fed once daily at 0800.
Comments Not Available
References
  • The rumen metabolome (in preparation)
Pathway Names Not Available
HMDB Pathways Not Available
KEGG Pathways Not Available
SimCell Pathways Not Available
General References
  1. Wikipedia Link Image
Metabolic Enzymes
  1. Poly(ADP-ribose) glycohydrolase ARH3
  2. Poly(ADP-ribose) glycohydrolase
Enzyme 1 [top]
Enzyme 1 ID 132
Enzyme 1 Name Poly(ADP-ribose) glycohydrolase ARH3
Enzyme 1 Synonyms
  1. ADP-ribosylhydrolase 3
  2. [Protein ADP-ribosylarginine] hydrolase-like protein 2
Enzyme 1 Gene Name ADPRHL2
Enzyme 1 Protein Sequence >Poly(ADP-ribose) glycohydrolase ARH3
MAAAAAMTAAGCGGAGAARSLSRFRGCLAGALLGDCVGAVYEARDTVDLTSVLRQVQDLE
PDPGSPGSARTEALCYTDDTAMARALVQSLLAKEAFDEVDMAHRFAQEYKKDPDRGYGAG
VITVFRKHLSPRCRDVFEPARAQFNGKGSYGNGGAMRVAGISLAYSSVQDVQKFARLSAQ
LTHASSLGYNGAILQALAVHLALQGESSSEHFLEQLLGHMEELESDAQSVLDARELGMEE
RPYSSRLKKIGELLEQDSVTREEVVSELGNGIAAFESVPTAIYCFLRCMEPDPEIPSTFN
SLQRTLVYSISLGGDTDTIATMAGAIAGAYYGMEQVPESWQQSCEGYEETDVLAQSLHRV
FQKSL
Enzyme 1 Number of Residues 365
Enzyme 1 Molecular Weight 39220.6
Enzyme 1 Theoretical pI 4.56
Enzyme 1 GO Classification
Function
Process
Component
Enzyme 1 General Function Posttranslational modification, protein turnover, chaperones
Enzyme 1 Specific Function Poly(ADP-ribose) synthesized after DNA damage is only present transiently and is rapidly degraded by poly(ADP-ribose) glycohydrolase. Poly(ADP-ribose) metabolism may be required for maintenance of the normal function of neuronal cells. Generates ADP-ribose from poly-(ADP-ribose), but does not hydrolyze ADP- ribose-arginine, -cysteine, -diphthamide, or -asparagine bonds
Enzyme 1 Pathways Not Available
Enzyme 1 Reactions Not Available
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • None
Enzyme 1 Transmembrane Regions
  • None
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 74268242 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID Q3SYV9 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name ARHL2_BOVIN Link Image
Enzyme 1 PDB ID Not Available
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >1098 bp
ATGGCGGCGGCGGCAGCGATGACGGCGGCGGGCTGCGGAGGGGCTGGGGCGGCACGCTCC
CTCTCCCGCTTCCGAGGCTGCCTGGCAGGCGCGCTGCTCGGGGACTGCGTGGGCGCCGTC
TACGAGGCGCGCGACACCGTCGACCTGACGTCAGTCCTGCGTCAGGTCCAGGATTTGGAG
CCGGACCCCGGCTCTCCCGGGAGCGCGCGGACAGAAGCACTGTGCTACACGGACGACACA
GCCATGGCCAGGGCGCTGGTGCAGTCCCTGCTGGCCAAGGAGGCCTTCGACGAGGTGGAC
ATGGCTCACAGGTTTGCTCAGGAGTACAAGAAGGACCCTGACCGGGGTTACGGTGCTGGA
GTGATCACCGTCTTCAGGAAACACCTAAGCCCCAGATGCCGGGATGTCTTTGAGCCTGCA
CGCGCCCAGTTCAATGGCAAAGGCTCCTACGGCAACGGGGGTGCCATGCGGGTGGCCGGC
ATCTCCCTGGCCTATAGCAGCGTGCAGGATGTGCAGAAGTTCGCCCGGCTCTCGGCCCAG
CTGACACACGCCTCCTCCCTGGGTTACAATGGTGCCATCCTGCAGGCCCTGGCTGTGCAC
CTGGCCTTGCAGGGCGAGTCGTCCAGTGAGCACTTCCTCGAGCAGCTCCTTGGCCACATG
GAAGAGCTGGAGAGTGATGCCCAGTCCGTGCTGGATGCCAGGGAGTTGGGCATGGAGGAG
CGTCCGTACTCCAGCCGACTGAAGAAGATCGGGGAGCTTCTAGAGCAGGACTCAGTGACC
AGAGAGGAGGTGGTGTCCGAGCTAGGAAATGGCATTGCTGCCTTTGAATCTGTGCCCACC
GCCATCTATTGCTTCCTGCGCTGCATGGAGCCCGACCCCGAGATCCCCTCTACCTTCAAC
AGCCTCCAAAGGACTCTCGTCTATTCCATCTCGCTCGGTGGGGACACGGACACCATTGCC
ACCATGGCCGGGGCCATTGCTGGCGCCTACTATGGGATGGAACAGGTGCCAGAGAGCTGG
CAGCAAAGCTGTGAAGGCTATGAGGAGACTGACGTCCTGGCCCAGAGCCTGCACCGGGTC
TTCCAGAAGAGTCTTTGA
Enzyme 1 GenBank Gene ID BC103360 Link Image
Enzyme 1 GeneCard ID ADPRHL2 Link Image
Enzyme 1 GenAtlas ID Not Available
Enzyme 1 HGNC ID Not Available
Enzyme 1 Chromosome Location Chromosome:1
Enzyme 1 Locus 1p34.3
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References Not Available
Enzyme 1 Metabolite References Not Available
Enzyme 2 [top]
Enzyme 2 ID 135
Enzyme 2 Name Poly(ADP-ribose) glycohydrolase
Enzyme 2 Synonyms Not Available
Enzyme 2 Gene Name PARG
Enzyme 2 Protein Sequence >Poly(ADP-ribose) glycohydrolase
MSAGPGCEPCTKRPRWDAAATSPPAASDARSFPGRQRRVLDSKDAPVQFRVPPSSSGCAL
GRAGQHRGSATSLVFKQKTITSWMDTKGIKTVESESLHSKENNNTREESMMSSVQKDNFY
QHNMEKLENVSQLGFDKSPVEKGTQYLKQHQTAAMCKWQNEGPHSERLLESEPPAVTLVP
EQFSNANVDQSSPKDDHSDTNSEESRDNQQFLTHVKLANAKQTMEDEQGREARSHQKCGK
ACHPAEACAGCQQEETDVVSESPLSDTGSEDVGTGLKNANRLNRQESSLGNSPPFEKESE
PESPMDVDNSKNSCQDSEADEETSPGFDEQEDSSSAQTANKPSRFQPREADTELRKRSSA
KGGEIRLHFQFEGGESRAGMNDVNAKRPGSTSSLNVECRNSKQHGRKDSKITDHFMRVPK
AEDKRKEQCEMKHQRTERKIPKYIPPHLSPDKKWLGTPIEEMRRMPRCGIRLPPLRPSAN
HTVTIRVDLLRIGEVPKPFPTHFKDLWDNKHVKMPCSEQNLYPVEDENGERAAGSRWELI
QTALLNRLTRPQNLKDAILKYNVAYSKKWDFTALIDFWDKVLEEAEAQHLYQSILPDMVK
IALCLPNICTQPIPLLKQKMNHSITMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDI
NFNRLFEGRSSRKPEKLKTLFCYFRRVTEKKPTGLVTFTRQSLEDFPEWERCEKLLTRLH
VTYEGTIEGNGQGMLQVDFANRFVGGGVTSAGLVQEEIRFLINPELIVSRLFTEVLDHNE
CLIITGTEQYSEYTGYAETYRWARSHEDRSERDDWQRRTTEIVAIDALHFRRYLDQFVPE
KIRRELNKAYCGFLRPGVSSENLSAVATGNWGCGAFGGDARLKALIQILAAAVAERDVVY
FTFGDSELMRDIYSMHTFLTERKLTVGEVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHA
VESCTQTTNQPGQRTGA
Enzyme 2 Number of Residues 977
Enzyme 2 Molecular Weight 110836.5
Enzyme 2 Theoretical pI 7.03
Enzyme 2 GO Classification
Function
Process
Component
Enzyme 2 General Function Involved in poly(ADP-ribose) glycohydrolase activity
Enzyme 2 Specific Function Poly(ADP-ribose) synthesized after DNA damage is only present transiently and is rapidly degraded by poly(ADP-ribose) glycohydrolase. Poly(ADP-ribose) metabolism may be required for maintenance of the normal function of neuronal cells
Enzyme 2 Pathways Not Available
Enzyme 2 Reactions Not Available
Enzyme 2 Pfam Domain Function
Enzyme 2 Signals
  • None
Enzyme 2 Transmembrane Regions
  • None
Enzyme 2 Essentiality Not Available
Enzyme 2 GenBank ID Protein 2062407 Link Image
Enzyme 2 UniProtKB/Swiss-Prot ID O02776 Link Image
Enzyme 2 UniProtKB/Swiss-Prot Entry Name PARG_BOVIN Link Image
Enzyme 2 PDB ID Not Available
Enzyme 2 Cellular Location Not Available
Enzyme 2 Gene Sequence >2934 bp
ATGAGTGCGGGCCCCGGCTGTGAGCCCTGCACCAAGCGACCCCGCTGGGACGCCGCTGCA
ACTTCTCCGCCGGCCGCCTCGGACGCCCGGAGCTTCCCCGGCAGGCAGAGGCGCGTCCTC
GATTCCAAGGACGCTCCGGTGCAGTTCAGGGTCCCGCCGTCCTCGTCAGGCTGCGCCCTG
GGCCGGGCGGGACAGCACCGAGGCAGCGCCACCTCTCTTGTTTTCAAACAGAAGACTATA
ACCAGTTGGATGGACACTAAAGGAATCAAGACAGTTGAATCAGAAAGTTTGCATAGTAAA
GAAAACAACAATACAAGAGAAGAATCCATGATGAGTTCTGTACAAAAAGATAACTTTTAT
CAACATAACATGGAAAAATTAGAAAATGTTTCTCAGCTAGGTTTTGATAAGTCACCAGTT
GAAAAAGGTACACAGTATTTGAAGCAGCATCAGACTGCGGCTATGTGTAAGTGGCAGAAT
GAAGGGCCACACTCAGAACGGCTTTTGGAAAGTGAACCTCCAGCGGTAACTCTGGTACCA
GAGCAGTTCAGTAATGCTAATGTCGATCAGTCGTCCCCAAAGGATGATCACAGTGACACA
AATAGTGAGGAGAGTAGAGATAATCAGCAGTTTTTGACACATGTAAAGCTTGCGAATGCA
AAGCAGACGATGGAAGATGAACAGGGCAGAGAAGCCAGAAGCCACCAGAAGTGTGGCAAG
GCTTGCCATCCTGCAGAAGCCTGTGCAGGGTGTCAGCAGGAGGAGACAGACGTGGTGTCC
GAGAGCCCCTTGTCGGACACTGGCTCTGAGGATGTTGGTACTGGACTGAAAAATGCCAAC
AGATTGAATAGACAAGAAAGTAGTCTAGGAAATTCTCCTCCATTTGAGAAAGAAAGTGAA
CCTGAGTCACCAATGGATGTAGATAATTCCAAAAATAGTTGTCAGGATTCAGAAGCAGAT
GAAGAGACAAGTCCAGGTTTTGATGAACAGGAAGATAGCAGTTCTGCTCAAACAGCAAAT
AAACCTTCAAGGTTCCAACCAAGAGAAGCTGACACTGAGTTGAGGAAGCGGTCCTCTGCT
AAGGGAGGTGAGATTCGATTACATTTCCAATTTGAAGGAGGAGAGAGTCGAGCTGGAATG
AATGATGTGAATGCCAAACGACCTGGAAGTACTTCTAGCCTGAATGTAGAGTGCAGAAAT
TCTAAGCAACATGGGAGAAAGGATTCTAAAATCACAGATCATTTCATGAGAGTGCCCAAA
GCAGAGGACAAAAGAAAAGAACAATGTGAAATGAAACATCAAAGAACAGAAAGGAAGATC
CCTAAATACATTCCACCTCACCTTTCTCCAGATAAGAAATGGCTTGGAACTCCTATTGAG
GAGATGAGGAGAATGCCAAGGTGTGGGATCCGGCTGCCTCCCTTGAGACCATCTGCCAAT
CACACAGTGACTATTCGGGTAGATCTTTTGCGAATAGGAGAAGTTCCTAAACCTTTCCCA
ACACATTTTAAAGATTTGTGGGACAACAAGCATGTTAAGATGCCTTGTTCAGAACAAAAC
TTGTACCCTGTGGAAGATGAGAATGGTGAGCGAGCTGCAGGCAGCCGGTGGGAACTCATT
CAGACTGCACTTCTCAACAGGCTCACTCGGCCCCAGAACCTGAAGGATGCTATTCTGAAG
TACAATGTGGCATATTCTAAGAAATGGGACTTTACAGCTTTGATTGATTTCTGGGATAAG
GTACTAGAAGAAGCAGAAGCTCAACACTTGTATCAGTCCATCTTGCCTGATATGGTGAAA
ATTGCACTCTGTCTGCCAAATATTTGTACCCAGCCAATACCACTCCTGAAACAGAAGATG
AATCATTCCATCACAATGTCACAGGAACAGATTGCCAGTCTTTTAGCTAATGCTTTCTTC
TGCACGTTTCCACGACGCAATGCCAAGATGAAATCAGAGTATTCCAGTTATCCAGATATT
AACTTCAATCGGTTGTTTGAAGGACGTTCATCAAGGAAACCAGAGAAGCTTAAAACGCTC
TTCTGCTACTTTAGAAGAGTCACAGAGAAAAAACCCACTGGGTTGGTGACATTCACAAGA
CAGAGTCTTGAAGATTTTCCAGAGTGGGAAAGATGTGAAAAACTCCTGACTCGACTGCAT
GTCACTTACGAAGGTACCATAGAAGGAAACGGCCAGGGCATGCTACAGGTGGATTTTGCA
AACCGTTTCGTTGGAGGTGGTGTAACCAGTGCAGGACTTGTGCAAGAAGAAATCCGCTTT
TTAATCAACCCTGAGTTGATTGTTTCACGGCTCTTCACTGAGGTGCTGGATCACAATGAA
TGTCTTATCATCACAGGTACTGAGCAGTACAGTGAATACACAGGCTATGCCGAAACATAC
CGCTGGGCCCGGAGCCATGAAGACAGGAGCGAAAGGGACGACTGGCAGAGGCGCACGACT
GAGATCGTCGCCATCGACGCCCTCCACTTCAGACGCTACCTCGACCAGTTTGTGCCCGAG
AAGATCAGACGGGAGCTTAACAAGGCTTACTGTGGATTTCTTCGTCCTGGAGTTTCTTCA
GAGAACCTGTCTGCAGTGGCTACAGGAAACTGGGGCTGTGGTGCCTTTGGGGGTGATGCT
AGACTAAAAGCCTTAATACAGATCCTGGCAGCTGCTGTAGCTGAGCGAGACGTGGTTTAT
TTCACCTTTGGGGACTCAGAACTGATGAGAGACATTTACAGCATGCATACATTCCTCACT
GAGAGGAAACTGACTGTTGGAGAAGTATATAAGCTGCTGCTACGATATTACAATGAAGAA
TGCAGAAACTGCTCCACCCCCGGACCAGACATCAAGCTTTATCCATTCATATACCATGCA
GTTGAGTCCTGTACACAGACCACCAACCAGCCGGGACAAAGGACGGGGGCCTGA
Enzyme 2 GenBank Gene ID U78975 Link Image
Enzyme 2 GeneCard ID PARG Link Image
Enzyme 2 GenAtlas ID Not Available
Enzyme 2 HGNC ID Not Available
Enzyme 2 Chromosome Location Chromosome:1
Enzyme 2 Locus 10q11.23
Enzyme 2 SNPs SNPJam Report Link Image
Enzyme 2 General References
  1. [PubMed Link Image]
Enzyme 2 Metabolite References Not Available