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Human Metabolome Database Version 2.5

 

Showing metabocard for D-Urobilinogen (HMDB04158)

Legend: metabolite field enzyme field

Version 2.5
Creation Date 2006-08-13 14:17:12
Update Date 2009-05-05 21:00:00
Accession Number HMDB04158
Secondary Accession Numbers Not Available
Common Name D-Urobilinogen
Description Urobilinogen is a colourless product of bilirubin reduction. It is formed in the intestines by bacterial action. Some urobilinogen is reabsorbed, taken up by the hepatocytes into the circulation and excreted by the kidney. This constitutes the normal "intrahepatic urobilinogen cycle". Increased amounts of bilirubin are formed in haemolysis which generates increased urobilinogen in the gut. In liver disease (such as hepatitis) the intrahepatic urobilinogen cycle is inhibited also increasing urobilinogen levels. Urobilinogen is converted to the yellow pigmented urobilin apparent in urine. The urobilinogen remaining in the intestine (stercobilinogen) is oxidized to brown stercobilin which gives the feces their characteristic color. In biliary obstruction, below normal amounts of conjugated bilirubin reach the intestine for conversion to urobilinogen. With limited urobilinogen available for reabsorption and excretion, the amount of urobilin found in the urine is low.
Synonyms
  1. Urobilinogen
  2. D-Urobilinogen
Chemical IUPAC Name 3-[2-[[3-(2-carboxyethyl)-5-[(4-ethenyl-3-methyl-5-oxo-1,2-dihydropyrrol-2-yl)methyl]-4-methyl-1H-pyrrol-2-yl]methyl]-5-[(3-ethyl-4-methyl-5-oxo-1,2-dihydropyrrol-2-yl)methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid
Chemical Formula C33H42N4O6
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Heterocyclic molecules
Class
  • Porphyrins
Sub Class
  • Bilirubins
Family
  • Mammalian Metabolite
Species
  • carboxylic acid
  • secondary carboxylic acid amide
  • lactam
  • alkene
  • aromatic compound
  • heterocyclic compound
Biofunction
—
Application
—
Source
  • Endogenous
Average Molecular Weight 590.710
Monoisotopic Molecular Weight 590.310425
Isomeric SMILES CCC1=C(C)C(=O)NC1CC1=C(C)C(CCC(O)=O)=C(CC2=C(CCC(O)=O)C(C)=C(CC3NC(=O)C(C=C)=C3C)N2)N1
Canonical SMILES CCC1=C(C)C(=O)NC1CC1=C(C)C(CCC(O)=O)=C(CC2=C(CCC(O)=O)C(C)=C(CC3NC(=O)C(C=C)=C3C)N2)N1
KEGG Compound ID C05791 Link Image
BioCyc ID Not Available
BiGG ID Not Available
Wikipedia Link Urobilinogen Link Image
NuGOwiki Link HMDB04158 Link Image
Metagene Link HMDB04158 Link Image
METLIN ID 7021 Link Image
PubChem Compound 440784 Link Image
PubChem Substance 7590379 Link Image
ChEBI ID Not Available
CAS Registry Number 17208-65-0
InChI Identifier InChI=1/C33H42N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h8,26-27,34-35H,2,7,9-15H2,1,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)
Synthesis Reference Watson, C. J.; Lowry, P. T. A further study of crystalline d-urobilin. Journal of Biological Chemistry (1956), 218 633-9.
Melting Point (Experimental) Not Available
Experimental Water Solubility Not Available Source: PhysProp
Predicted Water Solubility 0.020499999 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge -2
State Solid
Experimental LogP/Hydrophobicity Not Available Source: PhysProp
Predicted LogP/Hydrophobicity 2.77 [Predicted by ALOGPS]; 1.1 [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
  • Membrane (Predicted from LogP)
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
Porphyrin Metabolism SMP00024 Link Image map00860 Link Image
General References
  1. Binder L, Smith D, Kupka T, Nelson B, Glass B, Wainscott M, Haynes J: Failure of prediction of liver function test abnormalities with the urine urobilinogen and urine bilirubin assays. Arch Pathol Lab Med. 1989 Jan;113(1):73-6. [PubMed Link Image]
  2. Wikipedia Link Image
Metabolic Enzymes
  1. Beta-glucuronidase precursor
Enzyme 1 [top]
Enzyme 1 ID 6120
Enzyme 1 Name Beta-glucuronidase precursor
Enzyme 1 Synonyms
  1. Beta-G1
Enzyme 1 Gene Name GUSB
Enzyme 1 Protein Sequence >Beta-glucuronidase precursor 
MARGSAVAWAALGPLLWGCALGLQGGMLYPQESPSRECKELDGLWSFRADFSDNRRRGFE
EQWYRRPLWESGPTVDMPVPSSFNDISQDWRLRHFVGWVWYEREVILPERWTQDLRTRVV
LRIGSAHSYAIVWVNGVDTLEHEGGYLPFEADISNLVQVGPLPSRLRITIAINNTLTPTT
LPPGTIQYLTDTSKYPKGYFVQNTYFDFFNYAGLQRSVLLYTTPTTYIDDITVTTSVEQD
SGLVNYQISVKGSNLFKLEVRLLDAENKVVANGTGTQGQLKVPGVSLWWPYLMHERPAYL
YSLEVQLTAQTSLGPVSDFYTLPVGIRTVAVTKSQFLINGKPFYFHGVNKHEDADIRGKG
FDWPLLVKDFNLLRWLGANAFRTSHYPYAEEVMQMCDRYGIVVIDECPGVGLALPQFFNN
VSLHHHMQVMEEVVRRDKNHPAVVMWSVANEPASHLESAGYYLKMVIAHTKSLDPSRPVT
FVSNSNYAADKGAPYVDVICLNSYYSWYHDYGHLELIQLQLATQFENWYKKYQKPIIQSE
YGAETIAGFHQDPPLMFTEEYQKSLLEQYHLGLDQKRRKYVVGELIWNFADFMTEQSPTR
VLGNKKGIFTRQRQPKSAAFLLRERYWKIANETRYPHSVAKSQCLENSLFT
Enzyme 1 Number of Residues 651
Enzyme 1 Molecular Weight 74733
Enzyme 1 Theoretical pI 7.02
Enzyme 1 GO Classification
Function
  • catalytic activity
  • hydrolase activity
  • hydrolase activity, acting on glycosyl bonds
  • hydrolase activity, hydrolyzing O-glycosyl compounds
Process
  • carbohydrate metabolism
  • macromolecule metabolism
  • metabolism
  • physiological process
Component
—
Enzyme 1 General Function Carbohydrate transport and metabolism
Enzyme 1 Specific Function Plays an important role in the degradation of dermatan and keratan sulfates
Enzyme 1 Pathways
Enzyme 1 Reactions
  • a beta-D-glucuronoside + H2O = D-glucuronate + an alcohol
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • 1-22
Enzyme 1 Transmembrane Regions Not Available
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 183233 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID P08236 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name BGLR_HUMAN Link Image
Enzyme 1 PDB ID 1BHG Link Image
Enzyme 1 PDB File Show
Enzyme 1 3D Structure
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >1956 bp 
ATGGCCCGGGGGTCGGCGGTTGCCTGGGCGGCGCTCGGGCCGTTGTTGTGGGGCTGCGCG
CTGGGGCTGCAGGGCGGGATGCTGTACCCCCAGGAGAGCCCGTCGCGGGAGTGCAAGGAG
CTGGACGGCCTCTGGAGCTTCCGCGCCGACTTCTCTGACAACCGACGCCGGGGCTTCGAG
GAGCAGTGGTACCGGCGGCCGCTGTGGGAGTCAGGCCCCACCGTGGACATGCCAGTTCCC
TCCAGCTTCAATGACATCAGCCAGGACTGGCGTCTGCGGCATTTTGTCGGCTGGGTGTGG
TACGAACGGGAGGTGATCCTGCCGGAGCGATGGACCCAGGACCTGCGCACAAGAGTGGTG
CTGAGGATTGGCAGTGCCCATTCCTATGCCATCGTGTGGGTGAATGGGGTCGACACGCTA
GAGCATGAGGGGGGCTACCTCCCCTTCGAGGCCGACATCAGCAACCTGGTCCAGGTGGGG
CCCCTGCCCTCCCGGCTCCGAATCACTATCGCCATCAACAACACACTCACCCCCACCACC
CTGCCACCAGGGACCATCCAATACCTGACTGACACCTCCAAGTATCCCAAGGGTTACTTT
GTCCAGAACACATATTTTGACTTTTTCAACTACGCTGGACTGCAGCGGTCTGTACTTCTG
TACACGACACCCACCACCTACATCGATGACATCACCGTCACCACCAGCGTGGAGCAAGAC
AGTGGGCTGGTGAATTACCAGATCTCTGTCAAGGGCAGTAACCTGTTCAAGTTGGAAGTG
CGTCTTTTGGATGCAGAAAACAAAGTCGTGGCGAATGGGACTGGGACCCAGGGCCAACTT
AAGGTGCCAGGTGTCAGCCTCTGGTGGCCGTACCTGATGCACGAACGCCCTGCCTATCTG
TATTCATTGGAGGTGCAGCTGACTGCACAGACGTCACTGGGGCCTGTGTCTGACTTCTAC
ACACTCCCTGTGGGGATCCGCACTGTGGCTGTCACCAAGAGCCAGTTCCTCATCAATGGG
AAACCTTTCTATTTCCACGGTGTCAACAAGCATGAGGATGCGGACATCCGAGGGAAGGGC
TTCGACTGGCCGCTGCTGGTGAAGGACTTCAACCTGCTTCGCTGGCTTGGTGCCAACGCT
TTCCGTACCAGCCACTACCCCTATGCAGAGGAAGTGATGCAGATGTGTGACCGCTATGGG
ATTGTGGTCATCGATGAGTGTCCCGGCGTGGGCCTGGCGCTGCCGCAGTTCTTCAACAAC
GTTTCTCTGCATCACCACATGCAGGTGATGGAAGAAGTGGTGCGTAGGGACAAGAACCAC
CCCGCGGTCGTGATGTGGTCTGTGGCCAACGAGCCTGCGTCCCACCTAGAATCTGCTGGC
TACTACTTGAAGATGGTGATCGCTCACACCAAATCCTTGGACCCCTCCCGGCCTGTGACC
TTTGTGAGCAACTCTAACTATGCAGCAGACAAGGGGGCTCCGTATGTGGATGTGATCTGT
TTGAACAGCTACTACTCTTGGTATCACGACTACGGGCACCTGGAGTTGATTCAGCTGCAG
CTGGCCACCCAGTTTGAGAACTGGTATAAGAAGTATCAGAAGCCCATTATTCAGAGCGAG
TATGGAGCAGAAACGATTGCAGGGTTTCACCAGGATCCACCTCTGATGTTCACTGAAGAG
TACCAGAAAAGTCTGCTAGAGCAGTACCATCTGGGTCTGGATCAAAAACGCAGAAAATAT
GTGGTTGGAGAGCTCATTTGGAATTTTGCCGATTTCATGACTGAACAGTCACCGACGAGA
GTGCTGGGGAATAAAAAGGGGATCTTCACTCGGCAGAGACAACCAAAAAGTGCAGCGTTC
CTTTTGCGAGAGAGATACTGGAAGATTGCCAATGAAACCAGGTATCCCCACTCAGTAGCC
AAGTCACAATGTTTGGAAAACAGCCCGTTTACTTGA
Enzyme 1 GenBank Gene ID M15182 Link Image
Enzyme 1 GeneCard ID GUSB Link Image
Enzyme 1 GenAtlas ID GUSB Link Image
Enzyme 1 HGNC ID HGNC:4696 Link Image
Enzyme 1 Chromosome Location 7
Enzyme 1 Locus 7q21.11
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References
  1. Oshima A, Kyle JW, Miller RD, Hoffmann JW, Powell PP, Grubb JH, Sly WS, Tropak M, Guise KS, Gravel RA: Cloning, sequencing, and expression of cDNA for human beta-glucuronidase. Proc Natl Acad Sci U S A. 1987 Feb;84(3):685-9. [PubMed Link Image]
  2. Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK: The DNA sequence of human chromosome 7. Nature. 2003 Jul 10;424(6945):157-64. [PubMed Link Image]
  3. Shipley JM, Miller RD, Wu BM, Grubb JH, Christensen SG, Kyle JW, Sly WS: Analysis of the 5' flanking region of the human beta-glucuronidase gene. Genomics. 1991 Aug;10(4):1009-18. [PubMed Link Image]
  4. Tanaka J, Gasa S, Sakurada K, Miyazaki T, Kasai M, Makita A: Characterization of the subunits and sugar moiety of human placental and leukemic beta-glucuronidase. Biol Chem Hoppe Seyler. 1992 Jan;373(1):57-62. [PubMed Link Image]
  5. Guise KS, Korneluk RG, Waye J, Lamhonwah AM, Quan F, Palmer R, Ganschow RE, Sly WS, Gravel RA: Isolation and expression in Escherichia coli of a cDNA clone encoding human beta-glucuronidase. Gene. 1985;34(1):105-10. [PubMed Link Image]
  6. Zhang H, Li XJ, Martin DB, Aebersold R: Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol. 2003 Jun;21(6):660-6. Epub 2003 May 18. [PubMed Link Image]
  7. Jain S, Drendel WB, Chen ZW, Mathews FS, Sly WS, Grubb JH: Structure of human beta-glucuronidase reveals candidate lysosomal targeting and active-site motifs. Nat Struct Biol. 1996 Apr;3(4):375-81. [PubMed Link Image]
  8. Vervoort R, Lissens W, Liebaers I: Molecular analysis of a patient with hydrops fetalis caused by beta-glucuronidase deficiency, and evidence for additional pseudogenes. Hum Mutat. 1993;2(6):443-5. [PubMed Link Image]
  9. Wu BM, Sly WS: Mutational studies in a patient with the hydrops fetalis form of mucopolysaccharidosis type VII. Hum Mutat. 1993;2(6):446-57. [PubMed Link Image]
  10. Tomatsu S, Fukuda S, Sukegawa K, Ikedo Y, Yamada S, Yamada Y, Sasaki T, Okamoto H, Kuwahara T, Yamaguchi S, et al.: Mucopolysaccharidosis type VII: characterization of mutations and molecular heterogeneity. Am J Hum Genet. 1991 Jan;48(1):89-96. [PubMed Link Image]
  11. Shipley JM, Klinkenberg M, Wu BM, Bachinsky DR, Grubb JH, Sly WS: Mutational analysis of a patient with mucopolysaccharidosis type VII, and identification of pseudogenes. Am J Hum Genet. 1993 Mar;52(3):517-26. [PubMed Link Image]
Enzyme 1 Metabolite References Not Available