2.0 2012-05-31 13:59:58 -0600 2015-09-13 12:56:13 -0600 ECMDB03581 M2MDB000517 Dethiobiotin Dethiobiotin is a synthetic metabolite that mimic the effects of biotin on gene expression and thus have biotin-like activities. It is an intermediate in biotin metabolism, and converted to biotin via biotin synthase (EC:2.8.1.6). (KEGG) Biotin serves as a coenzyme for carboxylases such as propionyl-CoA carboxylase. (PMID 12730407) Desthiobiotin DTB C10H18N2O3 214.2615 214.131742452 6-[(4R,5S)-5-methyl-2-oxoimidazolidin-4-yl]hexanoic acid (4R,5S)-dethiobiotin 533-48-2 [H][C@@]1(C)NC(=O)N[C@]1([H])CCCCCC(O)=O InChI=1S/C10H18N2O3/c1-7-8(12-10(15)11-7)5-3-2-4-6-9(13)14/h7-8H,2-6H2,1H3,(H,13,14)(H2,11,12,15)/t7-,8+/m0/s1 AUTOLBMXDDTRRT-JGVFFNPUSA-N Solid Cytosol logp 0.72 ALOGPS logs -2.23 ALOGPS solubility 1.27e+00 g/l ALOGPS melting_point 157 oC logp 0.73 ChemAxon pka_strongest_acidic 4.63 ChemAxon pka_strongest_basic -1.8 ChemAxon iupac 6-[(4R,5S)-5-methyl-2-oxoimidazolidin-4-yl]hexanoic acid ChemAxon average_mass 214.2615 ChemAxon mono_mass 214.131742452 ChemAxon smiles [H][C@@]1(C)NC(=O)N[C@]1([H])CCCCCC(O)=O ChemAxon formula C10H18N2O3 ChemAxon inchi InChI=1S/C10H18N2O3/c1-7-8(12-10(15)11-7)5-3-2-4-6-9(13)14/h7-8H,2-6H2,1H3,(H,13,14)(H2,11,12,15)/t7-,8+/m0/s1 ChemAxon inchikey AUTOLBMXDDTRRT-JGVFFNPUSA-N ChemAxon polar_surface_area 78.43 ChemAxon refractivity 54.4 ChemAxon polarizability 23.15 ChemAxon rotatable_bond_count 6 ChemAxon acceptor_count 3 ChemAxon donor_count 3 ChemAxon physiological_charge -1 ChemAxon formal_charge 0 ChemAxon Biotin metabolism Biotin (vitamin H or vitamin B7) is the essential cofactor of biotin-dependent carboxylases, such as pyruvate carboxylase and acetyl-CoA carboxylase.In E. coli and many organisms, pimelate thioester is derived from malonyl-ACP. The pathway starts with a malonyl-[acp] interacting with S-adenosylmethionine through a biotin synthesis protein BioC resulting in a S-adenosylhomocysteine and a malonyl-[acp] methyl ester. The latter compound is then involved in the synthesis of a 3-ketoglutaryl-[acp] methyl ester through a 3-oxoacyl-[acyl-carrier-protein] synthase. The compound 3-ketoglutaryl-[acp] methyl ester is reduced by a NADPH mediated 3-oxoacyl-[acyl-carrier-protein] reductase resulting in a 3R-hydroxyglutaryl-[acp] methyl ester. This compound is then dehydrated through ad (3R)-hydroxymyristoyl-[acp] dehydratase producing a enoylglutaryl-[acp] methyl ester. This compound is then reduced through a NADPH mediated enoyl-acp-reductase [NADH] resulting in a glutaryl-[acp] methyl ester. This compound interacts with a malonyl-[acp] through a 3-oxoacyl-[acp] synthase 2 resulting in a 3-ketopimeloyl [acp] methyl ester. This compound is then reduced through a NADPH 3-oxoacyl [acp] reductase producing a 3-hydroxypimeloyl-[acp] methyl ester and then dehydrated by (3R)-hydroxymyristoyl-[acp] dehydratase to produce a enoylpimeloyl-[acp] methyl ester. This compound is then reduced by a NADPH dependent enoyl-[acp]reductase resulting in a pimeloyl-[acp] methyl ester. This compound then reacts with water through a carboxylesterase resulting in a pimeloyl-[acp] and a methanol. The pimeloyl-acp reacts with L-alanine through a 8-amino-7-oxononanoate synthase resulting in 8-amino-7-oxononanoate which in turn reacts with S-adenosylmethionine through a 7,8 diaminonanoate transaminase resulting in a S-adenosyl-4-methylthio-2-oxobutanoate and 7,8 diaminononanoate. The latter compound is then dephosphorylated through a dethiobiotin synthetase resulting in a dethiobiotin. This compound interacts with a sulfurated[sulfur carrier), a hydrogen ion and a S-adenosylmethionine through a biotin synthase to produce Biotin and releasing l-methionine and a 5-deoxyadenosine. Biotin is then metabolized by a bifunctional protein resulting in pyrophosphate and Biotinyl-5-AMP which in turn reacts with the same protein (bifunctional protein birA resulting ina biotin caroxyl carrying protein.This product then enters the fatty acid biosynthesis. PW000762 ec00780 Metabolic Metabolic pathways eco01100 biotin biosynthesis from 7-keto-8-aminopelargonate PWY0-1507 Specdb::CMs 1886 Specdb::CMs 2351 Specdb::CMs 30510 Specdb::CMs 31470 Specdb::CMs 38635 Specdb::CMs 137197 Specdb::CMs 144931 Specdb::NmrOneD 4757 Specdb::NmrOneD 4758 Specdb::NmrOneD 315341 Specdb::NmrOneD 315342 Specdb::NmrOneD 315343 Specdb::NmrOneD 315344 Specdb::NmrOneD 315345 Specdb::NmrOneD 315346 Specdb::NmrOneD 315347 Specdb::NmrOneD 315348 Specdb::NmrOneD 315349 Specdb::NmrOneD 315350 Specdb::NmrOneD 315351 Specdb::NmrOneD 315352 Specdb::NmrOneD 315353 Specdb::NmrOneD 315354 Specdb::NmrOneD 315355 Specdb::NmrOneD 315356 Specdb::NmrOneD 315357 Specdb::NmrOneD 315358 Specdb::NmrOneD 315359 Specdb::NmrOneD 315360 Specdb::MsMs 25019 Specdb::MsMs 25020 Specdb::MsMs 25021 Specdb::MsMs 31577 Specdb::MsMs 31578 Specdb::MsMs 31579 Specdb::MsMs 374815 Specdb::MsMs 446034 Specdb::MsMs 446035 Specdb::MsMs 446036 Specdb::MsMs 446037 Specdb::MsMs 447254 Specdb::MsMs 451501 Specdb::MsMs 2236383 Specdb::MsMs 2236981 Specdb::MsMs 2238550 Specdb::MsMs 2239047 Specdb::MsMs 2240511 Specdb::MsMs 2241176 Specdb::MsMs 2242576 Specdb::MsMs 2243285 Specdb::MsMs 2355789 Specdb::MsMs 2355790 Specdb::MsMs 2355791 Specdb::MsMs 2607264 HMDB03581 643 392787 C01909 16691 DETHIOBIOTIN DTB Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. 21097882 Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. 22080510 van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. 17765195 Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. 18331064 Rodriguez-Melendez, R., Lewis, B., McMahon, R. J., Zempleni, J. (2003). "Diaminobiotin and desthiobiotin have biotin-like activities in Jurkat cells." J Nutr 133:1259-1264. 12730407 Kuzuhara, Hiroyoshi; Ohrui, Hiroshi; Emoto, Sakae. Syntheses with azido sugars. II. Conversion of D-glucose to (+)-dethiobiotin. Agricultural and Biological Chemistry (1971), 35(1), 8-17. http://hmdb.ca/system/metabolites/msds/000/003/162/original/HMDB03581.pdf?1358462377 Putative dethiobiotin synthetase P0A6E9 BIOD2_ECOLI ynfK http://ecmdb.ca/proteins/P0A6E9.xml Biotin synthase P12996 BIOB_ECOLI bioB http://ecmdb.ca/proteins/P12996.xml Dethiobiotin synthetase P13000 BIOD_ECOLI bioD http://ecmdb.ca/proteins/P13000.xml [2Fe-2S] iron-sulfur cluster + S-Adenosylmethionine + Dethiobiotin > [2Fe-1S] desulfurated iron-sulfur cluster + Biotin + 5'-Deoxyadenosine + Hydrogen ion + L-Methionine Adenosine triphosphate + Carbon dioxide + 7,8-Diaminononanoate <> ADP + Dethiobiotin +3 Hydrogen ion + Phosphate R03182 DETHIOBIOTIN-SYN-RXN Dethiobiotin + Sulfur donor + 2 S-Adenosylmethionine + 2 e- + 2 Hydrogen ion <> Biotin +2 L-Methionine +2 5'-Deoxyadenosine R01078 Adenosine triphosphate + 7,8-Diaminononanoate + Carbon dioxide <> ADP + Phosphate + Dethiobiotin R03182 <i>S</i>-sulfanyl-[acceptor] + Dethiobiotin + S-Adenosylmethionine > an unsulfurated sulfur acceptor + Biotin + 5'-Deoxyadenosine + L-Methionine + Hydrogen ion 2.8.1.6-RXN Carbon dioxide + 7,8-Diaminononanoate + Adenosine triphosphate > Hydrogen ion + Dethiobiotin + Phosphate + ADP DETHIOBIOTIN-SYN-RXN Dethiobiotin + Hydrogen sulfide + 2 S-adenosyl-L-methionine > Biotin +2 L-Methionine +2 5'-Deoxyadenosine Adenosine triphosphate + 7,8-Diaminononanoate + Carbon dioxide > ADP + Inorganic phosphate + Dethiobiotin 7,8-Diaminononanoate + Adenosine triphosphate + Carbon dioxide + 7,8-Diaminononanoate > Dethiobiotin + Adenosine diphosphate + Phosphate + ADP PW_R002498 Dethiobiotin + 2 S-adenosyl-L-methionine + 2 Hydrogen ion + a sulfurated [sulfur carrier] > Biotin +2 L-Methionine +2 5'-Deoxyadenosine PW_R002499 Dethiobiotin + Sulfur donor + 2 S-Adenosylmethionine + 2 e- + 2 Hydrogen ion <> Biotin +2 L-Methionine +2 5'-Deoxyadenosine Adenosine triphosphate + Carbon dioxide + 7 7,8-Diaminononanoate <> ADP + Dethiobiotin +3 Hydrogen ion + Phosphate Dethiobiotin + Sulfur donor + 2 S-Adenosylmethionine + 2 e- + 2 Hydrogen ion <> Biotin +2 L-Methionine +2 5'-Deoxyadenosine Adenosine triphosphate + Carbon dioxide + 7 7,8-Diaminononanoate <> ADP + Dethiobiotin +3 Hydrogen ion + Phosphate