{"ymdb_id":"YMDB00620","created_at":"2011-05-29T18:36:49.000Z","updated_at":"2016-09-08T18:35:41.000Z","name":"N-(24-hydroxytetracosanoyl)sphinganine","cas":null,"state":null,"melting_point":null,"description":"\u003cp\u003eN-(24-Hydroxytetracosanoyl)sphinganine is a ceramide (a sphingolipid). Ceramides are found in high concentrations within the cell membrane of cells. Ceramides are composed of a sphingosine and a fatty acid. Ceramides are found in high concentrations within the cell membrane of cells. Caramides are known to promote transport of secretory vesicles from the ER to the Golgi apparatus. Sphingolipids like ceramide play import roles in lipid rafts which in yeast are responsible for delivering and sorting membrane bound proteins. Lipid rafts also play roles in membrane fusion during mating.[PMID: 16730802]\n\u003c/p\u003e\n\u003cp\u003e\nThere are three major pathways of ceramide generation. The sphingomyelinase pathway uses an enzyme to breakdown IPC, MIPC and M(IP)2C in the cell membrane and release ceramide. The de novo pathway creates ceramide from less complex molecules. Ceramide generation can also occur through breakdown of complex sphingolipids that are ultimately broken down into sphingosine, which is then reused by reacylation to form ceramide. This latter pathway is termed the Salvage pathway.[Wikipedia, PMID: 16730802]\n\u003c/p\u003e","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"Golgi;endoplasmic reticulum","synthesis_reference":null,"chebi_id":"52371","hmdb_id":null,"kegg_id":null,"pubchem_id":null,"cs_id":"23106994","foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"N-[(2S,3R)-1,3-dihydroxyoctadecan-2-yl]-24-hydroxytetracosanamide","traditional_iupac":"N-[(2S,3R)-1,3-dihydroxyoctadecan-2-yl]-24-hydroxytetracosanamide","logp":"13.191240043666667","pka":"14.492196702047824","alogps_solubility":"4.19e-05 g/l","alogps_logp":"9.79","alogps_logs":"-7.20","acceptor_count":"4","donor_count":"4","rotatable_bond_count":"40","polar_surface_area":"89.79","refractivity":"203.54979999999998","polarizability":"91.79603298742173","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"0.037754875836708","pka_strongest_acidic":"13.831978572939391","bioavailability":"0","number_of_rings":"0","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["cer2'_24","ceramide-2' (sphinganine:N-C24:2OH)","N-(2-hydroxytetracosanyl)-dihydrosphingosine"],"pathways":[],"growth_conditions":[],"references":[{"pubmed_id":18846089,"citation":"Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). \"A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.\" Nat Biotechnol 26:1155-1160."},{"pubmed_id":12484746,"citation":"Funato, K., Vallee, B., Riezman, H. (2002). \"Biosynthesis and trafficking of sphingolipids in the yeast Saccharomyces cerevisiae.\" Biochemistry 41:15105-15114."},{"pubmed_id":9804825,"citation":"Reggiori, F., Conzelmann, A. (1998). \"Biosynthesis of inositol phosphoceramides and remodeling of glycosylphosphatidylinositol anchors in Saccharomyces cerevisiae are mediated by different enzymes.\" J Biol Chem 273:30550-30559."},{"pubmed_id":18296751,"citation":"Dickson, R. C. (2008). \"Thematic review series: sphingolipids. New insights into sphingolipid metabolism and function in budding yeast.\" J Lipid Res 49:909-921."}],"proteins":[{"created_at":"2011-05-27T07:58:49.000Z","updated_at":"2011-07-22T17:54:25.000Z","name":"Ceramide very long chain fatty acid hydroxylase SCS7","uniprot_id":"Q03529","uniprot_name":"SCS7_YEAST","enzyme":true,"transporter":false,"gene_name":"SCS7","num_residues":384,"molecular_weight":"44881.10156","theoretical_pi":"6.55","general_function":"Involved in heme binding","specific_function":"Ceramide hydroxylase involved in the alpha-hydroxylation of sphingolipid-associated very long chain fatty acids. Hydroxylates the very long chain fatty acid of ceramides at C2 and C3","reactions":[{"id":1371,"direction":"\u003e","locations":"endoplasmic reticulum","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1373,"direction":"\u003e","locations":"endoplasmic reticulum","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1378,"direction":"\u003e","locations":"endoplasmic reticulum","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1379,"direction":"\u003e","locations":"endoplasmic reticulum","altext":null,"export":true,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"197-217;223-243;298-318;353-373","pdb_id":null,"cellular_location":"Endoplasmic reticulum membrane; Multi-pass membrane protein","genbank_gene_id":"AY693150","genbank_protein_id":"51013751","gene_card_id":"SCS7","chromosome_location":"chromosome 13","locus":"YMR272C","synonyms":["Ceramide VLCFA hydroxylase SCS7","Suppressor of calcium sensitivity 7"],"enzyme_classes":["1.-.-.-"],"go_classes":[{"category":"Component","description":" endoplasmic reticulum"},{"category":"Component","description":" organelle"},{"category":"Component","description":" membrane-bounded organelle"},{"category":"Component","description":" intracellular membrane-bounded organelle"},{"category":"Function","description":" iron ion binding"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" heme binding"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" ion binding"},{"category":"Function","description":" cation binding"},{"category":"Function","description":" metal ion binding"},{"category":"Function","description":" transition metal ion binding"},{"category":"Process","description":" fatty acid biosynthetic process"},{"category":"Process","description":" oxidation reduction"},{"category":"Process","description":" organic acid metabolic process"},{"category":"Process","description":" oxoacid metabolic process"},{"category":"Process","description":" carboxylic acid metabolic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" lipid metabolic process"},{"category":"Process","description":" primary metabolic process"},{"category":"Process","description":" cellular lipid metabolic process"},{"category":"Process","description":" membrane lipid metabolic process"},{"category":"Process","description":" sphingolipid metabolic process"},{"category":"Process","description":" monocarboxylic acid metabolic process"},{"category":"Process","description":" fatty acid metabolic process"}],"pfams":[{"name":"Cyt-b5","identifier":"PF00173"},{"name":"FA_hydroxylase","identifier":"PF04116"}],"pathways":[],"gene_sequence":"ATGTCGACTAATACTTCCAAGACTTTGGAACTGTTTTCAAAAAAGACGGTACAAGAACACAATACTGCCAATGACTGCTGGGTCACTTATCAAAACAGAAAGATTTATGACGTGACCAGGTTTTTGAGCGAACACCCTGGTGGTGACGAGTCCATCTTGGACTATGCTGGTAAGGACATTACTGAGATCATGAAAGACTCAGATGTGCATGAACACAGCGACTCCGCGTATGAAATCCTTGAGGACGAATATTTGATTGGTTACTTGGCAACTGACGAAGAGGCAGCGAGATTGTTGACTAACAAGAACCATAAGGTTGAAGTGCAGTTGTCAGCTGACGGTACTGAGTTTGACTCCACTACTTTTGTAAAGGAGTTGCCCGCCGAGGAGAAACTAAGTATTGCTACGGACTACAGTAACGACTACAAAAAGCATAAATTTTTGGATCTGAACCGTCCTTTGCTGATGCAGATTCTGCGTAGTGATTTCAAGAAAGATTTTTACGTTGACCAAATCCATAGACCAAGACATTACGGTAAGGGGTCTGCCCCGCTATTTGGTAATTTCTTGGAACCATTAACTAAAACAGCTTGGTGGGTTGTTCCAGTTGCTTGGTTGCCTGTAGTTGTGTACCACATGGGTGTTGCTTTGAAGAACATGAACCAGCTATTTGCATGTTTCTTGTTCTGTGTCGGTGTCTTTGTTTGGACTTTGATTGAATACGGTCTTCACCGTTTCCTATTTCATTTCGATGATTGGTTACCTGAAAGTAACATCGCATTCGCCACACATTTTCTACTACATGGTTGCCATCATTACTTGCCCATGGACAAGTACCGTTTAGTTATGCCACCTACTCTGTTCGTCATCCTTTGTGCTCCATTTTACAAGTTGGTATTTGCTCTGCTGCCACTTTATTGGGCTTACGCTGGTTTTGCTGGCGGTCTTTTCGGTTATGTCTGTTATGACGAATGTCATTTCTTCTTGCACCACTCTAAATTGCCTCCCTTCATGCGTAAGTTGAAAAAATATCACCTGGAACATCATTATAAAAACTACCAACTGGGATTTGGCGTCACATCCTGGTTTTGGGACGAAGTTTTTGGCACCTACTTAGGCCCCGATGCCCCATTGTCCAAAATGAAATATGAATAA","protein_sequence":"MSTNTSKTLELFSKKTVQEHNTANDCWVTYQNRKIYDVTRFLSEHPGGDESILDYAGKDITEIMKDSDVHEHSDSAYEILEDEYLIGYLATDEEAARLLTNKNHKVEVQLSADGTEFDSTTFVKELPAEEKLSIATDYSNDYKKHKFLDLNRPLLMQILRSDFKKDFYVDQIHRPRHYGKGSAPLFGNFLEPLTKTAWWVVPVAWLPVVVYHMGVALKNMNQLFACFLFCVGVFVWTLIEYGLHRFLFHFDDWLPESNIAFATHFLLHGCHHYLPMDKYRLVMPPTLFVILCAPFYKLVFALLPLYWAYAGFAGGLFGYVCYDECHFFLHHSKLPPFMRKLKKYHLEHHYKNYQLGFGVTSWFWDEVFGTYLGPDAPLSKMKYE"},{"created_at":"2011-05-27T09:13:37.000Z","updated_at":"2011-05-27T15:01:30.000Z","name":"Inositol phosphorylceramide synthase","uniprot_id":"P36107","uniprot_name":"AUR1_YEAST","enzyme":true,"transporter":false,"gene_name":"AUR1","num_residues":401,"molecular_weight":"45192.80078","theoretical_pi":"6.02","general_function":"Involved in catalytic activity","specific_function":"Catalyzes the addition of a phosphorylinositol group onto ceramide to form inositol phosphorylceramide, an essential step in sphingolipid biosynthesis","reactions":[{"id":1668,"direction":"\u003c\u003e","locations":"Golgi","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1669,"direction":"\u003c\u003e","locations":"Golgi","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1670,"direction":"\u003c\u003e","locations":"Golgi","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1671,"direction":"\u003c\u003e","locations":"Golgi","altext":null,"export":true,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"42-62;65-85;88-108;156-176;179-199;246-266;269-289;292-312","pdb_id":null,"cellular_location":"Golgi apparatus, Golgi stack membrane; Multi-pass membrane protein","genbank_gene_id":"U49090","genbank_protein_id":"1515352","gene_card_id":"AUR1","chromosome_location":"chromosome 11","locus":"YKL004W","synonyms":["IPC synthase","Aureobasidin A resistance protein","Phosphatidylinositol:ceramide phosphoinositol transferase"],"enzyme_classes":["2.-.-.-"],"go_classes":[{"category":"Component","description":" cell part"},{"category":"Component","description":" membrane"},{"category":"Function","description":" catalytic activity"},{"category":"Process","description":" Not Available"}],"pfams":[{"name":"PAP2","identifier":"PF01569"}],"pathways":[],"gene_sequence":"ATGGCAAACCCTTTTTCGAGATGGTTTCTATCAGAGAGACCTCCAAACTGCCATGTAGCCGATTTAGAAACAAGTTTAGATCCCCATCAAACGTTGTTGAAGGTGCAAAAATACAAACCCGCTTTAAGCGACTGGGTGCATTACATCTTCTTGGGATCCATCATGCTGTTTGTGTTCATTACTAATCCCGCACCTTGGATCTTCAAGATCCTTTTTTATTGTTTCTTGGGCACTTTATTCATCATTCCAGCTACGTCACAGTTTTTCTTCAATGCCTTGCCCATCCTAACATGGGTGGCGCTGTATTTCACTTCATCGTACTTTCCAGATGACCGCAGGCCTCCTATTACTGTCAAAGTGTTACCAGCGGTGGAAACAATTTTATACGGCGACAATTTAAGTGATATTCTTGCAACATCGACGAATTCCTTTTTGGACATTTTAGCATGGTTACCGTACGGACTATTTCATTATGGGGCCCCATTTGTCGTTGCTGCCATCTTATTCGTATTTGGTCCACCAACTGTTTTGCAAGGTTATGCTTTTGCATTTGGTTATATGAACCTGTTTGGTGTTATCATGCAAAATGTCTTTCCAGCCGCTCCCCCATGGTATAAAATTCTCTATGGATTGCAATCAGCCAACTATGATATGCATGGCTCGCCTGGTGGATTAGCTAGAATTGATAAGCTACTCGGTATTAATATGTATACTACAGCTTTTTCAAATTCCTCCGTCATTTTCGGTGCTTTTCCTTCACTGCATTCCGGGTGTGCTACTATGGAAGCCCTGTTTTTCTGTTATTGTTTTCCAAAATTGAAGCCCTTGTTTATTGCTTATGTTTGCTGGTTATGGTGGTCAACTATGTATCTGACACACCATTATTTTGTAGACCTTATGGCAGGTTCTGTGCTGTCATACGTTATTTTCCAGTACACAAAGTACACACATTTACCAATTGTAGATACATCTCTTTTTTGCAGATGGTCATACACTTCAATTGAGAAATACGATATATCAAAGAGTGATCCATTGGCTGCAGATTCAAACGATATCGAAAGTGTCCCTTTGTCCAACTTGGAACTTGACTTTGATCTTAATATGACTGATGAACCCAGTGTAAGCCCTTCGTTATTTGATGGATCTACTTCTGTTTCTCGTTCGTCCGCCACGTCTATAACGTCACTAGGTGTAAAGAGGGCTTAA","protein_sequence":"MANPFSRWFLSERPPNCHVADLETSLDPHQTLLKVQKYKPALSDWVHYIFLGSIMLFVFITNPAPWIFKILFYCFLGTLFIIPATSQFFFNALPILTWVALYFTSSYFPDDRRPPITVKVLPAVETILYGDNLSDILATSTNSFLDILAWLPYGLFHFGAPFVVAAILFVFGPPTVLQGYAFAFGYMNLFGVIMQNVFPAAPPWYKILYGLQSANYDMHGSPGGLARIDKLLGINMYTTAFSNSSVIFGAFPSLHSGCATMEALFFCYCFPKLKPLFIAYVCWLWWSTMYLTHHYFVDLMAGSVLSYVIFQYTKYTHLPIVDTSLFCRWSYTSIEKYDISKSDPLAADSNDIESVPLSNLELDFDLNMTDEPSVSPSLFDGSTSVSRSSATSITSLGVKRA"}]}