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Human Metabolome Database Version 2.5

 

Showing metabocard for Biocytin (HMDB03134)

Legend: metabolite field enzyme field

Version 2.5
Creation Date 2006-05-22 16:12:35
Update Date 2009-05-05 20:59:31
Accession Number HMDB03134
Secondary Accession Numbers Not Available
Common Name Biocytin
Description Biocytin is a naturally occurring low molecular weight analog of biotin, and a primary source of this essential metabolite for mammals. Biotinidase acts as a hydrolase by cleaving biocytin and biotinyl-peptides, thereby liberating biotin for reutilization. Mammals cannot synthesize biotin and, therefore, derive the vitamin from dietary sources or from the endogenous turnover of the carboxylases. Free biotin can readily enter the biotin pool, whereas holocarboxylases or other biotin-containing proteins must first be degraded proteolytically to biocytin (biotinyl-e-lysine) or biotinyl-peptides. Biocytin is also an especially versatile marker for neuroanatomical investigations, shown that may have multiple applications, especially for labeling neurons. (PMID: 8930409, 1384763, 2479450)
Synonyms
  1. Biotinyl-L-lysine
  2. H-Lys(biotinyl)-OH
  3. N-epsilon-Biotin-L-lysine
  4. N6-D-Biotinyl-L-lysine
  5. Ne-Biotynyl-L-lysine
  6. epsilon-N-Biotinyl-L-lysine
  7. N6-delta-Biotinyl-L-lysine
Chemical IUPAC Name (2S)-2-amino-6-[5-[(1S,2S,5R)-7-oxo-3-thia-6,8-diazabicyclo[3.3.0]oct-2-yl]pentanoylamino]hexanoic acid
Chemical Formula C16H28N4O4S
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Heterocyclic molecules
Class
  • Biotin and Derivatives
Sub Class
  • Conjugated biotins
Family
  • Mammalian Metabolite
Species
  • thioether
  • primary amine
  • primary aliphatic amine (alkylamine)
  • carboxylic acid
  • secondary carboxylic acid amide
  • urea
  • heterocyclic compound
  • alpha-aminoacid
Biofunction
—
Application
—
Source
  • Exogenous
Average Molecular Weight 372.483
Monoisotopic Molecular Weight 372.183136
Isomeric SMILES N[C@@H](CCCCNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)C(O)=O
Canonical SMILES NC(CCCCNC(=O)CCCCC1SCC2NC(=O)NC12)C(O)=O
KEGG Compound ID C05552 Link Image
BioCyc ID Not Available
BiGG ID 46012 Link Image
Wikipedia Link Not Available
NuGOwiki Link HMDB03134 Link Image
Metagene Link HMDB03134 Link Image
METLIN ID Not Available
PubChem Compound 83814 Link Image
PubChem Substance 10220364 Link Image
ChEBI ID Not Available
CAS Registry Number 576-19-2
InChI Identifier InChI=1/C16H28N4O4S/c17-10(15(22)23)5-3-4-8-18-13(21)7-2-1-6-12-14-11(9-25-12)19-16(24)20-14/h10-12,14H,1-9,17H2,(H,18,21)(H,22,23)(H2,19,20,24)/t10-,11-,12-,14-/m0/s1
Synthesis Reference Not Available
Melting Point (Experimental) 243 - 246 oC
Experimental Water Solubility Not Available Source: PhysProp
Predicted Water Solubility 0.17300001 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge 0
State Solid
Experimental LogP/Hydrophobicity Not Available Source: PhysProp
Predicted LogP/Hydrophobicity -0.69 [Predicted by ALOGPS]; -2.1 [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
Download FID (Varian)
Show Experimental Conditions Link Image
Experimental 13C NMR Spectrum Not Available
Experimental 13C HSQC Spectrum Download Spectrum
Download FID (Bruker)
Show Experimental Conditions Link Image
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
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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
  • mitochondria
  • nucleus
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
Biotin Metabolism SMP00066 Link Image map00780 Link Image
General References
  1. Spiga S, Fattore L, Puddu MC, Cappai A, Picciau S, Brotzu G, Serra GP, Petruzzo P: Use of biocytin as neuroanatomic tracer in harvested human pancreas: a confocal laser scanning microscopy analysis. Pancreas. 2002 May;24(4):329-35. [PubMed Link Image]
  2. Altemus KL, Lavenex P, Ishizuka N, Amaral DG: Morphological characteristics and electrophysiological properties of CA1 pyramidal neurons in macaque monkeys. Neuroscience. 2005;136(3):741-56. [PubMed Link Image]
  3. Evangelatos SA, Livaniou E, Kakabakos SE, Evangelatos GP, Ithakissios DS: Biotinidase radioassay using an 125I-biotin derivative, avidin, and polyethylene glycol reagents. Anal Biochem. 1991 Aug 1;196(2):385-9. [PubMed Link Image]
  4. Ebrahim H, Dakshinamurti K: Determination of biocytin. Anal Biochem. 1987 May 1;162(2):319-24. [PubMed Link Image]
  5. Suormala TM, Baumgartner ER, Bausch J, Holick W, Wick H: Quantitative determination of biocytin in urine of patients with biotinidase deficiency using high-performance liquid chromatography (HPLC). Clin Chim Acta. 1988 Oct 31;177(3):253-69. [PubMed Link Image]
  6. Hymes J, Fleischhauer K, Wolf B: Biotinylation of biotinidase following incubation with biocytin. Clin Chim Acta. 1995 Jan 16;233(1-2):39-45. [PubMed Link Image]
  7. Baur B, Suormala T, Bernoulli C, Baumgartner ER: Biotin determination by three different methods: specificity and application to urine and plasma ultrafiltrates of patients with and without disorders in biotin metabolism. Int J Vitam Nutr Res. 1998;68(5):300-8. [PubMed Link Image]
  8. van Gog FB, Visser GW, Gowrising RW, Snow GB, van Dongen GA: Synthesis and evaluation of 99mTc/99Tc-MAG3-biotin conjugates for antibody pretargeting strategies. Nucl Med Biol. 1998 Oct;25(7):611-9. [PubMed Link Image]
Metabolic Enzymes
  1. Biotinidase precursor
  2. Signal peptidase complex subunit 1
  3. cDNA, FLJ93758, Homo sapiens biotinidase (BTD), mRNA (Biotinidase, isoform CRA_a)
Enzyme 1 [top]
Enzyme 1 ID 5817
Enzyme 1 Name Biotinidase precursor
Enzyme 1 Synonyms Not Available
Enzyme 1 Gene Name BTD
Enzyme 1 Protein Sequence >Biotinidase precursor 
MSGARSKLALFLCGCYVVALGAHTGEESVADHHEAEYYVAAVYEHPSILSLNPLALISRQ
EALELMNQNLDIYEQQVMTAAQKDVQIIVFPEDGIHGFNFTRTSIYPFLDFMPSPQVVRW
NPCLEPHRFNDTEVLQRLSCMAIRGDMFLVANLGTKEPCHSSDPRCPKDGRYQFNTNVVF
SNNGTLVDRYRKHNLYFEAAFDVPLKVDLITFDTPFAGRFGIFTCFDILFFDPAIRVLRD
YKVKHVVYPTAWMNQLPLLAAIEIQKAFAVAFGINVLAANVHHPVLGMTGSGIHTPLESF
WYHDMENPKSHLIIAQVAKNPVGLIGAENATGETDPSHSKFLKILSGDPYCEKDAQEVHC
DEATKWNVNAPPTFHSEMMYDNFTLVPVWGKEGYLHVCSNGLCCYLLYERPTLSKELYAL
GVFDGLHTVHGTYYIQVCALVRCGGLGFDTCGQEITEATGIFEFHLWGNFSTSYIFPLFL
TSGMTLEVPDQLGWENDHYFLRKSRLSSGLVTAALYGRLYERD
Enzyme 1 Number of Residues 523
Enzyme 1 Molecular Weight 58914
Enzyme 1 Theoretical pI 5.72
Enzyme 1 GO Classification
Function
  • catalytic activity
  • hydrolase activity
  • hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
  • hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
  • hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
Process
  • metabolism
  • nitrogen compound metabolism
  • physiological process
Component
—
Enzyme 1 General Function Not Available
Enzyme 1 Specific Function Catalytic release of biotin from biocytin, the product of biotin-dependent carboxylases degradation
Enzyme 1 Pathways
Enzyme 1 Reactions
  • biotin amide + H2O = biotin + NH3
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • 1-21
Enzyme 1 Transmembrane Regions Not Available
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 468824 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID P43251 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name BTD_HUMAN Link Image
Enzyme 1 PDB ID Not Available
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >1632 bp 
ATGGCGCATGCGCATATTCAGGGCGGAAGGCGCGCTAAGAGCAGATTTGTGGTCTGCATT
ATGTCTGGAGCCAGAAGTAAGCTTGCTCTTTTCCTCTGCGGCTGTTACGTGGTTGCCCTG
GGAGCCCACACCGGGGAGGAGAGCGTGGCTGACCATCACGAGGCTGAATATTATGTGGCT
GCCGTGTATGAGCATCCATCCATCCTGAGTCTGAACCCTCTGGCTCTCATCAGCCGCCAA
GAGGCCTTGGAGCTCATGAACCAGAACCTTGACATCTATGAACAGCAAGTGATGACTGCA
GCCCAAAAGGATGTACAGATTATAGTGTTTCCAGAAGATGGCATTCATGGATTCAACTTT
ACAAGAACATCCATTTATCCATTTTTGGACTTCATGCCGTCTCCCCAGGTGGTCAGGTGG
AACCCATGCCTGGAGCCTCACCGCTTCAATGACACAGAGGTGCTCCAGCGCCTGAGTTGT
ATGGCCATCAGGGGAGATATGTTCTTGGTGGCCAATCTTGGGACAAAGGAGCCTTGTCAT
AGCAGTGACCCAAGGTGCCCAAAAGATGGGAGATACCAGTTCAACACAAATGTCGTGTTC
AGCAATAATGGAACCCTTGTTGACCGCTACCGTAAACACAACCTCTACTTTGAGGCAGCA
TTCGATGTTCCTCTTAAAGTGGATCTCATCACCTTTGATACCCCCTTTGCTGGCAGGTTT
GGCATCTTCACATGCTTTGATATATTGTTCTTTGACCCTGCCATCAGAGTCCTCAGAGAC
TACAAGGTGAAGCATGTTGTGTACCCAACTGCCTGGATGAACCAGCTCCCACTCTTGGCA
GCAATTGAGATTCAGAAAGCTTTTGCTGTTGCCTTTGGCATCAACGTTCTGGCAGCTAAT
GTCCACCACCCAGTTCTGGGGATGACAGGAAGTGGCATACACACCCCTCTGGAGTCCTTT
TGGTACCATGACATGGAAAATCCCAAAAGTCACCTTATAATTGCCCAGGTGGCCAAAAAT
CCAGTGGGTCTCATTGGTGCAGAGAATGCAACAGGTGAAACGGACCCATCCCATAGTAAG
TTTTTAAAAATTTTGTCAGGCGATCCGTACTGTGAGAAGGATGCTCAGGAAGTCCACTGT
GATGAGGCCACCAAGTGGAACGTGAATGCTCCTCCCACATTTCACTCTGAGATGATGTAT
GACAATTTCACCCTGGTCCCTGTCTGGGGAAAGGAAGGCTATCTCCACGTCTGTTCCAAT
GGCCTCTGCTGTTATTTACTTTACGAGAGGCCCACCTTATCCAAAGAGCTGTATGCCCTG
GGGGTCTTTGATGGGCTTCACACAGTACATGGCACTTACTACATCCAAGTGTGTGCCCTG
GTCAGGTGTGGGGGTCTTGGCTTCGACACCTGCGGACAGGAAATCACAGAGGCCACGGGG
ATATTTGAGTTTCACCTGTGGGGCAACTTCAGTACTTCCTATATCTTTCCTTTGTTTCTG
ACCTCAGGGATGACCCTAGAAGTCCCTGACCAGCTTGGCTGGGAGAATGACCACTATTTC
CTGAGGAAAAGTAGGCTGTCCTCTGGGCTGGTGACGGCGGCTCTCTATGGGCGCTTGTAT
GAGAGGGACTAG
Enzyme 1 GenBank Gene ID U03274 Link Image
Enzyme 1 GeneCard ID BTD Link Image
Enzyme 1 GenAtlas ID BTD Link Image
Enzyme 1 HGNC ID HGNC:1122 Link Image
Enzyme 1 Chromosome Location 3
Enzyme 1 Locus 3p25
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References
  1. Cole H, Reynolds TR, Lockyer JM, Buck GA, Denson T, Spence JE, Hymes J, Wolf B: Human serum biotinidase. cDNA cloning, sequence, and characterization. J Biol Chem. 1994 Mar 4;269(9):6566-70. [PubMed Link Image]
  2. Knight HC, Reynolds TR, Meyers GA, Pomponio RJ, Buck GA, Wolf B: Structure of the human biotinidase gene. Mamm Genome. 1998 Apr;9(4):327-30. [PubMed Link Image]
  3. Pomponio RJ, Norrgard KJ, Hymes J, Reynolds TR, Buck GA, Baumgartner R, Suormala T, Wolf B: Arg538 to Cys mutation in a CpG dinucleotide of the human biotinidase gene is the second most common cause of profound biotinidase deficiency in symptomatic children. Hum Genet. 1997 Apr;99(4):506-12. [PubMed Link Image]
  4. Swango KL, Demirkol M, Huner G, Pronicka E, Sykut-Cegielska J, Schulze A, Mayatepek E, Wolf B: Partial biotinidase deficiency is usually due to the D444H mutation in the biotinidase gene. Hum Genet. 1998 May;102(5):571-5. [PubMed Link Image]
Enzyme 1 Metabolite References Not Available
Enzyme 2 [top]
Enzyme 2 ID 10515
Enzyme 2 Name Signal peptidase complex subunit 1
Enzyme 2 Synonyms
  1. Microsomal signal peptidase 12 kDa subunit
  2. SPase 12 kDa subunit
Enzyme 2 Gene Name SPCS1
Enzyme 2 Protein Sequence >Signal peptidase complex subunit 1 
MLEHLSSLPTQMDYKGQKLAEQMFQGIILFSAIVGFIYGYVAEQFGWTVYIVMAGFAFSC
LLTLPPWPIYRRHPLKWLPVQESSTDDKKPGERKIKRHAKNN
Enzyme 2 Number of Residues 102
Enzyme 2 Molecular Weight 11805
Enzyme 2 Theoretical pI Not Available
Enzyme 2 GO Classification
Function
  • catalytic activity
  • hydrolase activity
  • peptidase activity
  • signal peptidase activity
Process
  • cellular metabolism
  • metabolism
  • peptide metabolism
  • physiological process
  • signal peptide processing
Component
  • cell
  • cell fraction
  • integral to membrane
  • intrinsic to membrane
  • membrane
  • membrane fraction
  • microsome
  • protein complex
  • signal peptidase complex
  • vesicular fraction
Enzyme 2 General Function Not Available
Enzyme 2 Specific Function Component of the microsomal signal peptidase complex which removes signal peptides from nascent proteins as they are translocated into the lumen of the endoplasmic reticulum
Enzyme 2 Pathways Not Available
Enzyme 2 Reactions
  • Protein N6,N6,N6-trimethyl-L-lysine + H2O --> peptide sans lysine + N6,N6,N6-Trimethyl-L-lysine
Enzyme 2 Pfam Domain Function
Enzyme 2 Signals
  • 1-39
Enzyme 2 Transmembrane Regions
  • 20-42 47-69
Enzyme 2 Essentiality Not Available
Enzyme 2 GenBank ID Protein 16905460 Link Image
Enzyme 2 UniProtKB/Swiss-Prot ID Q9Y6A9 Link Image
Enzyme 2 UniProtKB/Swiss-Prot Entry Name SPCS1_HUMAN Link Image
Enzyme 2 PDB ID Not Available
Enzyme 2 Cellular Location Not Available
Enzyme 2 Gene Sequence >309 bp 
ATGCTGGAGCATCTGAGCTCGCTGCCCACGCAGATGGATTACAAGGGCCAGAAGCTAGCT
GAACAGATGTTTCAGGGAATTTATCTTTTTTCTGCAATAGTTGGATTTATCTACGGGTAC
GTGGCTGAACAGTTCGGGTGGACTGTCTATATAGTTATGGCCGGATTTGCTTTTTCATGT
TTGCTGACACTTCCTCCATGGCCCATCTATCGCCGGCATCCTCTCAAGTGGTTACCTGTT
CAAGAATCAAGCACAGACGACAAGAAACCAGGGGAAAGAAAAATTAAGAGGCATGCTAAA
AATAATTGA
Enzyme 2 GenBank Gene ID L38852 Link Image
Enzyme 2 GeneCard ID SPCS1 Link Image
Enzyme 2 GenAtlas ID SPCS1 Link Image
Enzyme 2 HGNC ID HGNC:23401 Link Image
Enzyme 2 Chromosome Location 3
Enzyme 2 Locus 3p21.1
Enzyme 2 SNPs SNPJam Report Link Image
Enzyme 2 General References
  1. Kalies KU, Hartmann E: Membrane topology of the 12- and the 25-kDa subunits of the mammalian signal peptidase complex. J Biol Chem. 1996 Feb 16;271(7):3925-9. [PubMed Link Image]
  2. Zhang QH, Ye M, Wu XY, Ren SX, Zhao M, Zhao CJ, Fu G, Shen Y, Fan HY, Lu G, Zhong M, Xu XR, Han ZG, Zhang JW, Tao J, Huang QH, Zhou J, Hu GX, Gu J, Chen SJ, Chen Z: Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. Genome Res. 2000 Oct;10(10):1546-60. [PubMed Link Image]
Enzyme 2 Metabolite References Not Available
Enzyme 3 [top]
Enzyme 3 ID 16426
Enzyme 3 Name cDNA, FLJ93758, Homo sapiens biotinidase (BTD), mRNA (Biotinidase, isoform CRA_a)
Enzyme 3 Synonyms Not Available
Enzyme 3 Gene Name BTD
Enzyme 3 Protein Sequence >cDNA, FLJ93758, Homo sapiens biotinidase (BTD), mRNA (Biotinidase, isoform CRA_a) 
MAHAHIQGGRRAKSRFVVCIMSGARSKLALFLCGCYVVALGAHTGEESVADHHEAEYYVA
AVYEHPSILSLNPLALISRQEALELMNQNLDIYEQQVMTAAQKDVQIIVFPEDGIHGFNF
TRTSIYPFLDFMPSPQVVRWNPCLEPHRFNDTEVLQRLSCMAIRGDMFLVANLGTKEPCH
SSDPRCPKDGRYQFNTNVVFSNNGTLVDRYRKHNLYFEAAFDVPLKVDLITFDTPFAGRF
GIFTCFDILFFDPAIRVLRDYKVKHVVYPTAWMNQLPLLAAIEIQKAFAVAFGINVLAAN
VHHPVLGMTGSGIHTPLESFWYHDMENPKSHLIIAQVAKNPVGLIGAENATGETDPSHSK
FLKILSGDPYCEKDAQEVHCDEATKWNVNAPPTFHSEMMYDNFTLVPVWGKEGYLHVCSN
GLCCYLLYERPTLSKELYALGVFDGLHTVHGTYYIQVCALVRCGGLGFDTCGQEITEATG
IFEFHLWGNFSTSYIFPLFLTSGMTLEVPDQLGWENDHYFLRKSRLSSGLVTAALYGRLY
ERD
Enzyme 3 Number of Residues 543
Enzyme 3 Molecular Weight 61134
Enzyme 3 Theoretical pI 6.22
Enzyme 3 GO Classification
Function
  • catalytic activity
  • hydrolase activity
  • hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
  • hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
  • hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
Process
  • metabolism
  • nitrogen compound metabolism
  • physiological process
Component
—
Enzyme 3 General Function Not Available
Enzyme 3 Specific Function Not Available
Enzyme 3 Pathways Not Available
Enzyme 3 Reactions Not Available
Enzyme 3 Pfam Domain Function
Enzyme 3 Signals
  • None
Enzyme 3 Transmembrane Regions
  • None
Enzyme 3 Essentiality Not Available
Enzyme 3 GenBank ID Protein Not Available
Enzyme 3 UniProtKB/Swiss-Prot ID B2R865 Link Image
Enzyme 3 UniProtKB/Swiss-Prot Entry Name B2R865_HUMAN Link Image
Enzyme 3 PDB ID Not Available
Enzyme 3 Cellular Location Not Available
Enzyme 3 Gene Sequence Not Available
Enzyme 3 GenBank Gene ID AK313252 Link Image
Enzyme 3 GeneCard ID B2R865 Link Image
Enzyme 3 GenAtlas ID Not Available
Enzyme 3 HGNC ID Not Available
Enzyme 3 Chromosome Location Not Available
Enzyme 3 Locus Not Available
Enzyme 3 SNPs SNPJam Report Link Image
Enzyme 3 General References Not Available
Enzyme 3 Metabolite References Not Available