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Bovine Rumen Metabolome Database



Showing metabocard for Uracil (RMDB00300)

Legend: metabolite field enzyme field

Version 1.0
Creation Date 2005-11-16 15:48:42
Update Date 2009-08-12 13:44:00
Accession Number RMDB00300
Common Name Uracil
Description Uracil is a common naturally occurring pyrimidine found in RNA, it base pairs with adenine and is replaced by thymine in DNA. Methylation of uracil produces thymine. Uracil's use in the body is to help carry out the synthesis of many enzymes necessary for cell function through bonding with riboses and phosphates. Uracil serves as allosteric regulator and coenzyme for many important biochemical reactions. UDP and UTP regulate CPSase II activity in animals. UDP-glucose regulates the conversion of glucose to galactose in the liver and other tissues in the process of carbohydrate metabolism. Uracil is also involved in the biosynthesis of polysaccharides and the transportation of sugars containing aldehydes
Synonyms
  1. 2,4-Dihydroxypyrimidine
  2. 2,4-Dioxopyrimidine
  3. 2,4-Pyrimidinediol
  4. 2,4-Pyrimidinedione
  5. Hybar X
  6. Pirod
  7. Pyrod
  8. Uracil
Chemical IUPAC Name 2,4(1H,3H)-Pyrimidinedione
Chemical Formula C4H4N2O2
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Nucleosides and Nucleoside conjugates
Class
  • Pyrimidines and Derivatives
Sub Class
  • Hydroxy pyrimidines
Family
  • Mammalian_Metabolite
Species
  • oxo(het)arene; aromatic compound; heterocyclic compound
Biofunction
  • Component of beta-Alanine metabolism; Component of Pantothenate and CoA biosynthesis; Component of Pyrimidine metabolism
Application
Source
  • Endogenous
Average Molecular Weight 112.087
Monoisotopic Molecular Weight 112.027275
Isomeric SMILES O=C1NC=CC(=O)N1
Canonical SMILES O=C1NC=CC(=O)N1
KEGG Compound ID C00106 Link Image
BioCyc ID URACIL Link Image
BiGG ID 33879 Link Image
Wikipedia Link Uracil Link Image
METLIN ID 258 Link Image
PubChem Compound 1174 Link Image
PubChem Substance 6912247 Link Image
ChEBI ID 17568 Link Image
CAS Registry Number 66-22-8
InChI Identifier InChI=1/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)
Synthesis Reference Burckhalter, J. H.; Scarborough, Homer C. The synthesis of uracils as anticonvulsants. Journal of the American Pharmaceutical Association (1912-1977) (1955), 44 545-50.
Melting Point (Experimental) 330 oC
Experimental Water Solubility 3.6 mg/mL [YALKOWSKY,SH & DANNENFELSER,RM (1992)] Source: PhysProp
Predicted Water Solubility 26.5 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge 0
State Solid
Experimental LogP/Hydrophobicity -1.07 [HANSCH,C ET AL. (1995)] Source: PhysProp
Predicted LogP/Hydrophobicity -1.20 [Predicted by ALOGPS]; -0.9 [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 1BD4 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
Show Peaklist
Mass Spectrum
Low Energy
Download File
Show Experimental Conditions Link Image
Medium Energy
Download File
Show Experimental Conditions Link Image
High Energy
Download File
Show Experimental Conditions Link Image
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 103.5 +/- 25.2 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 120.8 +/- 39.9 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 122 +/- 127 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 199 +/- 91 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 246 +/- 48 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. Dihydropyrimidine dehydrogenase [NADP+]
  2. Uracil phosphoribosyltransferase
Enzyme 1 [top]
Enzyme 1 ID 689
Enzyme 1 Name Dihydropyrimidine dehydrogenase [NADP+]
Enzyme 1 Synonyms
  1. DHPDHase
  2. DPD
  3. Dihydrouracil dehydrogenase
  4. Dihydrothymine dehydrogenase
Enzyme 1 Gene Name DPYD
Enzyme 1 Protein Sequence >Dihydropyrimidine dehydrogenase [NADP+]
MAPVLSKDVADIESILALNPRTQSRATLRSTLAKKLDKKHWKRNPDKNCFNCEKLENNFD
DIKHTTLGERGALREAMRCLKCADAPCQKSCPTNLDIKSFITSISNKNYYGAAKMIFSDN
PLGLTCGMVCPTSDLCVGGCNLYATEEGPINIGGLQQYATEVFKAMNIPQIRNPSLPPPE
KMPEAYSAKIALLGAGPASISCASFLARLGYNDITIFEKQEYVGGISTSEIPQFRLPYDV
VNFEIELMKDLGVKIICGKSLSVNDITLSTLKEEGYKAAFIGIGLPEPKKDHIFQGLTQD
QGFYTSKDFLPLVAKSSKAGMCACHSPLLSIRGTVIVLGAGDTAFDCATSALRCGARRVF
IVFRKGFVNIRAVPEEVELAREEKCEFLPFLSPRKVIVKGGRIVAMQFVRTEQDETGKWN
EDGDQIACLKADVVISAFGSVLSDPKVKEALSPIKFNRWDLPEVDPETMQTSEPWVFAGG
DVVGIANTTVEAVNDGKQASWYIHRYIQSQYGASVSAKPELPLFYTPIDLVDISVEMAAL
KFTNPFGLASATPTTSSSMIRRAFEAGWAFALTKTFSLDKDIVTNVSPRIIRGTTSGPMY
GPGQSSFLNIELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNRNDWMELSRKAEAS
GADALELNLSCPHGMGERGMGLACGQDPELVRNICRWVRQAVRIPFFAKLTPNVTDIVSI
ARAAKEGGANGVTATNTVSGLMGLKADGTPWPAVGREKRTTYGGVSGTAIRPIALRAVTT
IARALPEFPILATGGIDSAESGLQFLHGGASVLQVCSAIQNQDFTIIQDYCTGLKALLYL
KSIEELQDWDGQSPATKSHQKGKPVPCIAELVGKKLPSFGPYLEKCKKIIAEEKLRLKKE
NVTVLPLERNHFIPKKPIPSVKDVIGKALQYLGTYGELNNTEQVVAVIDEEMCINCGKCY
MTCNDSGYQAIQFDPETHLPTVTDTCTGCTLCLSVCPIIDCIKMVSRTTPYEPKRGLPLA
VNPVS
Enzyme 1 Number of Residues 1025
Enzyme 1 Molecular Weight 111695.6
Enzyme 1 Theoretical pI 7.32
Enzyme 1 GO Classification
Function
Process
Component
Enzyme 1 General Function Amino acid transport and metabolism
Enzyme 1 Specific Function Involved in pyrimidine base degradation. Catalyzes the reduction of uracil and thymine
Enzyme 1 Pathways
  • Amino-acid biosynthesis
  • beta-alanine biosynthesis
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 677951 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID Q28007 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name DPYD_BOVIN Link Image
Enzyme 1 PDB ID 1GTE Link Image
Enzyme 1 PDB File Show
Enzyme 1 3D Structure
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >3078 bp
ATGGCCCCTGTGCTAAGCAAGGACGTGGCGGATATCGAGAGTATCCTGGCTTTAAATCCT
CGAACACAGTCTCGTGCAACTCTGCGTTCCACTTTGGCCAAGAAATTAGACAAGAAACAT
TGGAAAAGAAATCCTGATAAGAACTGCTTTAATTGCGAGAAGCTGGAGAATAATTTTGAT
GACATCAAGCACACGACTCTTGGTGAGCGAGGAGCTCTCCGAGAAGCAATGAGATGCCTG
AAATGTGCAGATGCCCCCTGTCAGAAGAGCTGTCCAACAAATCTAGATATCAAATCGTTC
ATCACAAGTATCTCAAACAAGAACTATTATGGAGCTGCTAAGATGATATTTTCTGACAAC
CCACTTGGTCTGACCTGTGGAATGGTATGCCCCACCTCTGATCTTTGTGTAGGTGGATGT
AATTTGTATGCCACTGAAGAGGGACCAATTAATATTGGTGGATTGCAGCAATATGCTACT
GAGGTATTCAAAGCAATGAATATCCCACAAATCAGGAATCCTTCTCTGCCTCCCCCAGAA
AAAATGCCTGAAGCCTATTCTGCAAAGATTGCTCTTTTGGGTGCTGGGCCTGCAAGTATA
AGTTGTGCTTCGTTCTTGGCTCGATTAGGCTACAATGACATCACTATATTTGAAAAACAA
GAATACGTTGGTGGTATAAGTACTTCTGAAATCCCTCAGTTCCGGCTGCCATATGATGTA
GTAAATTTTGAGATTGAGCTTATGAAGGACCTTGGTGTAAAGATAATTTGTGGTAAAAGC
CTTTCAGTGAATGACATTACTCTTAGTACTTTGAAAGAAGAAGGGTACAAAGCTGCTTTC
ATTGGGATAGGTTTGCCAGAACCCAAGAAGGATCACATCTTCCAAGGCCTGACACAGGAC
CAGGGGTTTTACACTTCCAAAGACTTTCTGCCTCTTGTAGCCAAAAGCAGTAAAGCAGGA
ATGTGCGCCTGTCACTCTCCATTGCTGTCGATACGGGGAACCGTGATTGTACTCGGAGCT
GGAGACACAGCTTTCGACTGTGCAACATCCGCTTTACGTTGTGGAGCCCGCCGAGTGTTC
ATCGTCTTCAGAAAAGGCTTTGTTAATATAAGAGCTGTCCCTGAGGAGGTGGAGCTTGCT
AGAGAAGAAAAATGTGAATTTTTGCCTTTCTTGTCTCCACGGAAGGTTATAGTAAAAGGT
GGGAGAATTGTTGCCATGCAATTTGTTCGGACAGAGCAAGATGAAACTGGAAAATGGAAT
GAAGATGGAGATCAGATAGCCTGTCTGAAAGCCGATGTGGTCATCAGTGCCTTTGGCTCA
GTTCTGAGTGATCCTAAAGTAAAAGAAGCCTTGAGCCCTATAAAATTTAACAGATGGGAT
CTCCCAGAAGTAGATCCAGAAACTATGCAAACCAGTGAGCCATGGGTGTTTGCAGGTGGT
GATGTGGTTGGTATAGCCAACACTACAGTGGAAGCCGTGAATGATGGAAAGCAAGCCTCT
TGGTACATTCACAGATATATACAGTCACAATATGGAGCTTCAGTTTCTGCTAAGCCCGAA
CTCCCCCTGTTTTATACTCCCATTGATCTGGTGGACATTAGTGTGGAAATGGCTGCATTG
AAGTTTACAAATCCTTTTGGTCTTGCCAGTGCAACTCCAACTACCAGTTCGTCAATGATT
CGAAGAGCTTTTGAAGCTGGATGGGCCTTTGCTCTGACCAAAACTTTCTCTCTTGATAAG
GATATAGTGACAAATGTTTCACCCAGAATCATCCGGGGGACCACCTCTGGCCCCATGTAT
GGCCCTGGACAAAGCTCTTTCCTGAATATTGAGCTCATCAGTGAAAAAACGGCTGCATAT
TGGTGTCAAAGTGTCACTGAACTAAAAGCCGACTTTCCAGACAATATTGTGATTGCTAGC
ATCATGTGCAGTTACAACAGAAATGACTGGATGGAACTCTCCAGAAAGGCTGAGGCTTCT
GGAGCAGACGCCCTGGAGTTAAATTTATCGTGTCCGCATGGCATGGGAGAAAGAGGAATG
GGTCTGGCTTGTGGACAGGATCCAGAGCTGGTGCGGAACATCTGTCGCTGGGTTAGGCAA
GCTGTTCGGATTCCTTTTTTTGCCAAGTTGACCCCAAATGTCACTGATATTGTAAGCATA
GCCAGAGCTGCAAAGGAAGGTGGGGCAAATGGTGTTACAGCTACCAACACTGTCTCAGGT
CTCATGGGATTAAAAGCTGATGGCACACCCTGGCCAGCAGTGGGCCGTGAGAAGCGGACT
ACATACGGCGGAGTGTCCGGCACAGCCATCAGACCTATTGCTTTGAGAGCTGTGACCACC
ATTGCTCGTGCTTTGCCTGAATTTCCCATTTTGGCCACTGGTGGAATTGACTCAGCTGAA
AGTGGTCTTCAGTTTCTCCACGGTGGTGCTTCGGTGCTCCAGGTATGCAGTGCTATTCAA
AATCAGGATTTCACTATCATCCAAGACTACTGCACTGGCCTCAAAGCCTTGCTTTATCTG
AAAAGCATTGAAGAACTACAGGACTGGGATGGGCAGAGTCCAGCCACGAAGAGTCACCAG
AAAGGGAAACCAGTCCCTTGTATTGCTGAACTTGTGGGAAAGAAACTGCCAAGCTTTGGA
CCTTATCTTGAGAAGTGCAAGAAAATCATAGCAGAGGAAAAGTTGAGACTGAAAAAAGAA
AATGTGACCGTTCTACCACTTGAAAGAAACCATTTTATCCCAAAAAAACCTATTCCTTCT
GTTAAGGATGTGATTGGAAAAGCTCTGCAGTACCTTGGAACATATGGTGAACTGAACAAC
ACAGAGCAGGTTGTGGCTGTGATCGATGAAGAGATGTGTATCAACTGTGGCAAATGCTAC
ATGACCTGTAATGACTCTGGCTACCAGGCTATCCAGTTTGATCCTGAAACCCACCTGCCC
ACCGTTACTGACACTTGTACAGGCTGTACCCTGTGTCTCTCCGTCTGCCCTATTATCGAC
TGCATCAAAATGGTTTCCAGGACAACACCTTATGAACCAAAGAGAGGCTTGCCCTTGGCT
GTGAATCCTGTGTCTTAA
Enzyme 1 GenBank Gene ID U20981 Link Image
Enzyme 1 GeneCard ID DPYD Link Image
Enzyme 1 GenAtlas ID Not Available
Enzyme 1 HGNC ID Not Available
Enzyme 1 Chromosome Location Chromosome:1
Enzyme 1 Locus 1p22
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References
  1. [PubMed Link Image]
Enzyme 1 Metabolite References Not Available
Enzyme 2 [top]
Enzyme 2 ID 1107
Enzyme 2 Name Uracil phosphoribosyltransferase
Enzyme 2 Synonyms
  1. UMP pyrophosphorylase
  2. UPRTase
Enzyme 2 Gene Name UPRT
Enzyme 2 Protein Sequence >Uracil phosphoribosyltransferase
MATELRCPDSMPCHNQQVNSASTQNPEPQQAGDLILAHAGGNSDSAATLTLLSGHAHSSV
PAELDPQASGGATFNSENNGGTGNYDAPASDSLLGDCEISRQIGAQLKLLPMNDQIRELQ
TIIRDKTASRGDFMFSADRLIRLVVEEGLNQLPYEECMVTTPTGFKYEGVKFEKGNCGVS
IMRSGEAMEQGLRDCCRSIRIGKILIQSDEETQRAKVYYAKFPPDIYRRKVLLMYPILST
GNTVIEAVKVLIEHGVQPSVIILLSLFSTPHGAKSIIQEFPEITILTTEVHPVAPTHFGQ
KYFGTD
Enzyme 2 Number of Residues 306
Enzyme 2 Molecular Weight 33354.5
Enzyme 2 Theoretical pI 5.18
Enzyme 2 GO Classification
Function
Process
Component
Enzyme 2 General Function Nucleotide transport and metabolism
Enzyme 2 Specific Function UMP + diphosphate = uracil + 5-phospho-alpha- D-ribose 1-diphosphate
Enzyme 2 Pathways
  • Pyrimidine metabolism
  • UMP biosynthesis via salvage pathway
  • UMP from uracil:step 1/1
Enzyme 2 Reactions Not Available
Enzyme 2 Pfam Domain Function Not Available
Enzyme 2 Signals
  • None
Enzyme 2 Transmembrane Regions
  • None
Enzyme 2 Essentiality Not Available
Enzyme 2 GenBank ID Protein 81673864 Link Image
Enzyme 2 UniProtKB/Swiss-Prot ID Q32LA4 Link Image
Enzyme 2 UniProtKB/Swiss-Prot Entry Name UPP_BOVIN Link Image
Enzyme 2 PDB ID Not Available
Enzyme 2 Cellular Location Not Available
Enzyme 2 Gene Sequence >921 bp
ATGGCCACGGAGTTACGGTGTCCGGACTCCATGCCCTGTCACAATCAGCAAGTAAACTCT
GCCTCGACCCAAAACCCTGAGCCGCAGCAAGCTGGAGACCTGATCCTGGCCCACGCTGGG
GGAAACAGCGATTCCGCGGCCACGCTGACTCTCCTCAGCGGGCACGCCCATTCTAGCGTA
CCGGCTGAGCTGGACCCTCAGGCCTCCGGCGGCGCCACCTTCAACTCAGAAAACAACGGT
GGCACTGGCAACTATGACGCTCCAGCCAGCGATTCCCTCCTAGGGGACTGCGAAATCTCC
CGGCAGATCGGGGCCCAGCTTAAGCTTCTGCCAATGAATGATCAGATCCGGGAGCTGCAG
ACTATCATCAGGGACAAGACAGCCAGTAGAGGGGACTTCATGTTTTCTGCGGATCGTTTG
ATCAGACTTGTTGTGGAAGAGGGATTGAATCAGCTGCCATATGAAGAATGCATGGTGACC
ACTCCAACAGGGTTCAAGTATGAAGGCGTGAAATTTGAAAAGGGAAATTGTGGGGTCAGC
ATAATGAGAAGCGGTGAGGCCATGGAACAAGGTTTACGAGACTGCTGTCGATCCATACGA
ATTGGAAAGATCCTGATTCAGAGTGATGAGGAGACACAAAGAGCCAAAGTATATTATGCC
AAGTTCCCCCCAGACATTTACAGAAGAAAAGTCCTTCTGATGTATCCAATTCTCAGTACT
GGAAATACTGTAATTGAAGCTGTAAAGGTTCTCATAGAACATGGAGTTCAACCTAGTGTT
ATTATCCTACTCAGTCTGTTCTCCACTCCTCATGGTGCCAAATCAATCATTCAAGAGTTT
CCGGAGATCACAATTTTAACTACTGAAGTTCATCCTGTTGCACCTACACATTTCGGACAG
AAATACTTTGGAACAGACTAA
Enzyme 2 GenBank Gene ID BC109679 Link Image
Enzyme 2 GeneCard ID UPRT Link Image
Enzyme 2 GenAtlas ID Not Available
Enzyme 2 HGNC ID Not Available
Enzyme 2 Chromosome Location Not Available
Enzyme 2 Locus Xq13.3
Enzyme 2 SNPs SNPJam Report Link Image
Enzyme 2 General References Not Available
Enzyme 2 Metabolite References Not Available