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Bovine Metabolome Database



Showing metabocard for D-Xylose (BMDB00098)

Legend: metabolite field enzyme field

Version 1.0
Creation Date 2005-11-16 15:48:42
Update Date 2009-05-28 13:50:40
Accession Number BMDB00098
Common Name D-Xylose
Description Xylose or wood sugar is an aldopentose - a monosaccharide containing five carbon atoms and an aldehyde functional group. It has chemical formula C5H10O5 and is 40% as sweet as sucrose. Xylose is found in the embryos of most edible plants. The polysaccharide xylan, which is closely associated with cellulose, consists practically entirely of d-xylose. Corncobs, cottonseed hulls, pecan shells, and straw contain considerable amounts of this sugar. Xylose is also found in mucopolysaccharides of connective tissue and sometimes in the urine. Xylose is the first sugar added to serine or threonine residues during proteoglycan type O-glycosylation. Therefore xylose is involved in the biosythetic pathways of most anionic polysaccharides such as heparan sulphate and chondroitin sulphate. In medicine, xylose is used to test for malabsorption by administering a xylose solution to the patient after fasting. If xylose is detected in the blood and/or urine within the next few hours, it has been absorbed by the intestines. Xylose is said to be one of eight sugars which are essential for human nutrition, the others being galactose, glucose, mannose, N-acetylglucosamine, N-acetylgalactosamine, fucose, and sialic acid. (Wikipedia)
Synonyms
  1. d-Xylose
  2. Xylo-pfan
  3. Xyloside
  4. D-(+)-xylose
  5. Xylose
  6. Xylomed
  7. Wood sugar
  8. D-xylo-pentose
Chemical IUPAC Name (3R,4R,5R)-oxane-2,3,4,5-tetrol
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; secondary alcohol; 1,2-diol; heterocyclic compound
Biofunction
Application
Source
  • Endogenous
Average Molecular Weight 150.130
Monoisotopic Molecular Weight 150.052826
Isomeric SMILES O[C@@H]1COC(O)[C@H](O)[C@H]1O
Canonical SMILES OC1COC(O)C(O)C1O
KEGG Compound ID C00181 Link Image
BioCyc ID XYLOSE Link Image
BiGG ID 34162 Link Image
Wikipedia Link Wood sugar Link Image
METLIN ID 314 Link Image
PubChem Compound 135191 Link Image
PubChem Substance 24870807 Link Image
ChEBI ID 15936 Link Image
CAS Registry Number 58-86-6
InChI Identifier InChI=1/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4-,5?/m1/s1
Synthesis Reference Lavarack, B. P.; Griffin, G.; Rodman, D. Optimizing the autohydrolysis of bagasse to extract D-xylose. Proceedings of the Conference of the Australian Society of Sugar Cane Technologists (1999), 21st 394-400.
Melting Point (Experimental) 90.5 oC
Experimental Water Solubility 555.0 mg/mL [MERCK INDEX (1996)] Source: PhysProp
Predicted Water Solubility 1.22e+03 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge 0
State Solid
Experimental LogP/Hydrophobicity Not Available Source: PhysProp
Predicted LogP/Hydrophobicity -2.57 [Predicted by ALOGPS]; -1.9 [Predicted by PubChem via XLOGP] Calculated using ALOGPS
Material Safety Data Sheet (MSDS)
MOL File Show
SDF File Show
PDB File Show
2D Structure
3D Structure
Experimental PDB ID Not Available
Experimental 1H NMR Spectrum Download Spectrum
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Experimental 13C NMR Spectrum Download Spectrum
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Experimental 13C HSQC Spectrum Download Spectrum
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Predicted 1H NMR Spectrum Show Image
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Predicted 13C NMR Spectrum Show Image
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Mass Spectrum
Low Energy
Download File
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Medium Energy
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High Energy
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Simplified TOCSY Spectrum Show Image
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BMRB Spectrum Show Image
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Cellular Location
  • Cytoplasm
  • Extracellular
  • lysosome
Biofluid Location Not Available
Tissue Location
Tissue References
Erythrocyte
Small Intestine
Concentrations (Normal) Not Available
Concentrations (Abnormal) Not Available
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. Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase
  2. Sodium/myo-inositol cotransporter 2
Enzyme 1 [top]
Enzyme 1 ID 383
Enzyme 1 Name Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase
Enzyme 1 Synonyms
  1. Dimeric dihydrodiol dehydrogenase
  2. D-xylose-NADP dehydrogenase
  3. D-xylose 1-dehydrogenase
Enzyme 1 Gene Name DHDH
Enzyme 1 Protein Sequence >Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase
MALRWGIVSAGLISSDFTTMLRMLPRSEHQVVAVAARDLSRAKEFAKKHDIPKAYGSYEE
LAKDPDVEVAYIGTQHPQHKAAVLLCLTAGKAVLCEKPMGVNAAEVREMVAEARSRGLFF
MEAIWTRFFPAVEALRSVLAQGTLGDLRVVRAEFGKNLTHVHRATDWAQAGGGLLDLGIY
CLQFISMVFGGQKPEKISAVGRRHETGVDDTVTVILQYPGGVHGSFTCSISAQLSNTVSV
SGTKGMAQLLDPCWSPTELVVKGEHKEFPLPPAPGKEFNFTNGMGMSYEAKHVRECLQKG
LKESPVIPLVESELLADILEEVRKAIGITFPQDKH
Enzyme 1 Number of Residues 335
Enzyme 1 Molecular Weight 36583.0
Enzyme 1 Theoretical pI 7.33
Enzyme 1 GO Classification
Function
Process
Component
Enzyme 1 General Function Involved in binding
Enzyme 1 Specific Function Trans-1,2-dihydrobenzene-1,2-diol + NADP(+) = catechol + NADPH
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 109939774 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID Q148L6 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name DHDH_BOVIN Link Image
Enzyme 1 PDB ID Not Available
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >1008 bp
ATGGCGCTTCGCTGGGGCATCGTGTCGGCTGGCCTTATCTCCAGCGACTTCACGACGATG
CTGCGGATGCTGCCTCGCTCTGAGCACCAGGTAGTGGCGGTAGCGGCCCGTGACCTGAGC
CGGGCGAAGGAGTTTGCTAAGAAACACGACATCCCCAAGGCCTATGGATCCTATGAGGAA
CTGGCCAAGGACCCCGACGTGGAGGTGGCCTACATTGGCACCCAGCACCCCCAGCACAAG
GCCGCAGTGTTACTCTGCCTGACAGCGGGCAAGGCTGTGTTGTGCGAAAAGCCCATGGGT
GTGAACGCCGCGGAAGTGCGCGAAATGGTTGCTGAGGCCCGATCCCGAGGCCTCTTCTTT
ATGGAGGCCATCTGGACCCGGTTCTTCCCTGCTGTAGAGGCTCTGAGGTCTGTCCTGGCC
CAGGGAACTCTGGGGGACCTTCGGGTGGTTCGGGCAGAATTTGGGAAGAATCTCACCCAC
GTACACCGGGCCACAGACTGGGCCCAGGCGGGAGGTGGCTTGTTAGACCTTGGCATCTAC
TGCCTCCAGTTCATCTCCATGGTCTTCGGTGGGCAGAAGCCAGAGAAGATTTCAGCTGTG
GGAAGGCGCCATGAAACAGGTGTGGACGACACTGTCACTGTGATACTCCAGTACCCAGGA
GGGGTCCACGGCAGCTTCACCTGCAGCATCTCTGCCCAGCTCTCCAACACGGTGTCCGTG
AGTGGTACCAAGGGCATGGCCCAGCTCCTCGACCCCTGCTGGAGCCCAACAGAGCTGGTG
GTGAAGGGGGAGCATAAGGAGTTCCCACTGCCTCCAGCCCCAGGCAAGGAGTTCAATTTT
ACAAATGGAATGGGCATGAGTTATGAGGCCAAGCATGTCCGGGAATGCCTGCAGAAAGGC
CTGAAGGAAAGTCCTGTGATTCCTCTGGTGGAAAGTGAGCTCCTGGCTGACATCCTTGAG
GAGGTGAGGAAGGCCATTGGAATCACCTTCCCCCAAGACAAACACTGA
Enzyme 1 GenBank Gene ID BC118168 Link Image
Enzyme 1 GeneCard ID DHDH Link Image
Enzyme 1 GenAtlas ID Not Available
Enzyme 1 HGNC ID Not Available
Enzyme 1 Chromosome Location Chromosome:1
Enzyme 1 Locus 19q13.3
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 1874
Enzyme 2 Name Sodium/myo-inositol cotransporter 2
Enzyme 2 Synonyms
  1. Na+/myo-inositol cotransporter 2
  2. Solute carrier family 5 member 11
Enzyme 2 Gene Name SLC5A11
Enzyme 2 Protein Sequence >Sodium/myo-inositol cotransporter 2
MESSASSPPLTQSDPLEAFPRRTLEAGDIAVLVLYFLFVLAVGLWSTVKTKRDTVKGYFL
AGGNMLWWPVGASLFASNVGSGHFVGLAGSGAAAGLSVTAYELNGLFFVLMLSWIFLPIY
ITGQVTTMPEYLRKRFGGNRIPIILAVLYLFIYIFTKISVDMYAGAIFIQQSLHVNLYLA
IVGLLAVTALYTIAGGLAAVIYTDALQTLIMLIGALILMGYSFAAVGGLEGLEEKYFLAM
ASNRSGNSSCGLPREDAFHIFRDPVTSDLPWPGILFGMSIPSLWYWCTDQVIVQRTLAAK
NLSHAKGGSLMAAYLKVLPLFIMVFPGMVSRVLFPDEVACADPEICRKVCSNPAGCSDIA
YPKLVLELLPTGLRGLMMAVMVAALTSSLTSIFNSASTIFTMDLWNHLRPRASEKELMIV
GRVFVLLLVLVSILWIPVVQASQGGQLFIYIQSISSYLQPPVAVVFIMGCFWKRANEKGA
FFGLVLGLLLGLVRLILDFIYVQPRCDQLDERPAVVKDVHYLYFSMILSSVTLITVCAVS
WFTEPPSKEMVSRLTWFTRHDPVVQKEQVPSATPPPLTLSQNGTPEASGTNTQFEMVQEN
LSKTHSCDMTTKRSKVVKAILWLCGVENKGKEQAPSRADPIIVSLEENPLVKTLLDLNLI
ICISCAIFLWGYFA
Enzyme 2 Number of Residues 674
Enzyme 2 Molecular Weight 73956.4
Enzyme 2 Theoretical pI 7.59
Enzyme 2 GO Classification
Function
Process
Component
Enzyme 2 General Function Involved in sodium ion binding
Enzyme 2 Specific Function Involved in the sodium-dependent cotransport of myo- inositol (MI) with a Na(+):MI stoichiometry of 2:1. Exclusively responsible for apical MI transport and absorption in intestine. Also can transport D-chiro-inositol (DCI) but not L-fructose. Exhibits stereospecific cotransport of both D-glucose and D- xylose. May induce apoptosis through the TNF-alpha, PDCD1 pathway. May play a role in the regulation of MI concentration in serum, involving reabsorption in at least the proximal tubule of the kidney
Enzyme 2 Pathways Not Available
Enzyme 2 Reactions Not Available
Enzyme 2 Pfam Domain Function
Enzyme 2 Signals
  • None
Enzyme 2 Transmembrane Regions
  • 26-46 57-77 103-123 141-161 181-201 209-229 273-293 309-329 375-397 419-439 447-467 480-500 522-542 654-674
Enzyme 2 Essentiality Not Available
Enzyme 2 GenBank ID Protein 73587027 Link Image
Enzyme 2 UniProtKB/Swiss-Prot ID Q3ZC26 Link Image
Enzyme 2 UniProtKB/Swiss-Prot Entry Name SC5AB_BOVIN Link Image
Enzyme 2 PDB ID Not Available
Enzyme 2 Cellular Location Not Available
Enzyme 2 Gene Sequence >2025 bp
ATGGAGAGCAGCGCCAGCAGCCCTCCTCTCACACAGTCAGATCCCCTGGAGGCGTTTCCC
CGGAGGACGCTGGAAGCAGGAGACATCGCAGTGCTGGTTCTATATTTCCTCTTTGTCCTG
GCTGTTGGACTATGGTCCACAGTGAAGACCAAAAGAGACACCGTGAAAGGCTACTTTCTA
GCTGGAGGCAACATGCTGTGGTGGCCAGTGGGTGCATCCTTGTTTGCCAGCAACGTTGGA
AGTGGACATTTCGTTGGCCTGGCAGGGTCAGGTGCTGCTGCGGGTCTTTCTGTAACTGCT
TATGAGCTTAATGGCTTATTTTTCGTGCTGATGTTGTCCTGGATCTTCCTTCCAATCTAC
ATCACTGGTCAGGTCACCACGATGCCAGAGTACCTACGGAAACGTTTTGGTGGCAACAGG
ATTCCCATCATCCTGGCTGTGCTCTACCTGTTTATCTACATCTTCACCAAGATCTCGGTG
GACATGTATGCAGGCGCCATCTTCATTCAGCAGTCTTTGCATGTGAATCTCTACTTGGCC
ATAGTCGGGTTGCTGGCCGTCACAGCTCTATACACCATCGCAGGTGGCCTGGCAGCTGTG
ATCTACACGGATGCTCTACAGACTCTGATCATGCTTATAGGAGCGCTCATCCTGATGGGC
TACAGTTTTGCTGCAGTTGGTGGGTTGGAAGGCTTGGAGGAGAAATATTTTTTGGCAATG
GCCAGCAACCGGAGCGGGAACAGCAGCTGCGGGTTGCCCCGGGAAGATGCCTTCCATATT
TTCCGAGACCCAGTGACGTCTGATCTCCCATGGCCCGGGATCCTATTTGGAATGTCCATC
CCGTCTCTCTGGTATTGGTGCACGGATCAGGTGATTGTTCAGCGGACTCTGGCTGCCAAG
AACCTGTCCCACGCCAAAGGGGGCTCTCTGATGGCCGCATACCTGAAGGTGCTACCCCTT
TTCATCATGGTGTTCCCGGGTATGGTCAGCCGTGTCCTCTTTCCAGACGAAGTAGCTTGT
GCAGACCCAGAAATCTGCCGGAAGGTCTGTAGCAACCCCGCCGGCTGCTCTGACATCGCG
TATCCCAAACTTGTGCTGGAACTCCTGCCTACAGGGCTCCGTGGGCTCATGATGGCTGTG
ATGGTGGCGGCGCTCACGTCTTCCCTCACCTCCATCTTTAACAGTGCCAGCACCATCTTC
ACCATGGACCTCTGGAACCATCTCCGGCCTCGGGCATCTGAGAAGGAGCTCATGATTGTG
GGCAGGGTGTTTGTGTTGCTTCTGGTGTTGGTCTCCATCCTCTGGATCCCTGTGGTCCAG
GCCAGCCAGGGCGGCCAGCTCTTCATCTACATCCAGTCCATCAGCTCCTACCTACAGCCA
CCTGTGGCTGTGGTCTTCATCATGGGATGTTTCTGGAAGCGGGCCAATGAAAAGGGTGCC
TTCTTCGGTCTCGTCTTAGGCCTCCTCCTAGGCTTGGTTAGGCTGATCCTGGACTTCATT
TACGTGCAGCCTCGCTGTGACCAGCTGGATGAGCGCCCAGCCGTGGTAAAGGATGTCCAC
TACCTCTACTTCTCTATGATCCTGTCCTCGGTCACCCTGATCACAGTGTGTGCCGTGAGC
TGGTTCACAGAGCCGCCCTCCAAGGAAATGGTCAGTCGCTTGACCTGGTTTACTCGCCAT
GACCCCGTGGTCCAGAAGGAACAGGTGCCGTCAGCAACCCCACCGCCTCTTACCCTTTCT
CAAAACGGGACACCAGAGGCCAGCGGCACCAACACCCAGTTCGAGATGGTTCAAGAAAAC
CTGTCCAAAACCCACAGCTGCGACATGACCACAAAGCGGTCCAAAGTGGTGAAAGCCATC
TTGTGGCTCTGTGGGGTGGAGAACAAGGGCAAGGAGCAAGCACCCAGCAGAGCGGACCCG
ATCATAGTTTCCCTGGAAGAAAACCCCTTGGTGAAAACCCTTCTGGACCTCAACCTCATC
ATTTGCATCAGCTGTGCCATATTTCTCTGGGGCTACTTTGCTTAA
Enzyme 2 GenBank Gene ID BC102962 Link Image
Enzyme 2 GeneCard ID SLC5A11 Link Image
Enzyme 2 GenAtlas ID Not Available
Enzyme 2 HGNC ID Not Available
Enzyme 2 Chromosome Location Chromosome:1
Enzyme 2 Locus 16pter-p11
Enzyme 2 SNPs SNPJam Report Link Image
Enzyme 2 General References Not Available
Enzyme 2 Metabolite References Not Available