2.0 2012-05-31 13:46:11 -0600 2015-06-03 15:53:46 -0600 ECMDB01137 M2MDB000271 Hydroxymethylbilane Hydroxymethylbilane is a molecule involved in the metabolism of porphyrin. In the third step, it is generated by the enzyme porphobilinogen deaminase , and in the next step the enzyme uroporphyrinogen I synthase converts it into uroporphyrinogen I. -- Wikipedia 3,8,13,18-Tetrakis(carboxymethyl)-19-(hydroxymethyl)bilane-2,7,12,17-tetrapropanoate 3,8,13,18-Tetrakis(carboxymethyl)-19-(hydroxymethyl)bilane-2,7,12,17-tetrapropanoic acid 3,8,13,18-Tetrakis(carboxymethyl)-5,10,15,22,23,24-hexahydro-19-(hydroxymethyl)-21H-Biline-2,7,12,17-tetrapropanoate 3,8,13,18-Tetrakis(carboxymethyl)-5,10,15,22,23,24-hexahydro-19-(hydroxymethyl)-21H-Biline-2,7,12,17-tetrapropanoic acid 3-[2-[[4-(2-Carboxyethyl)-5-[[4-(2-carboxyethyl)-5-[[4-(2-carboxyethyl)-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-4-(carboxymethyl)-5-(hydroxymethyl)-1H-pyrrol-3-yl]propanoate 3-[2-[[4-(2-Carboxyethyl)-5-[[4-(2-carboxyethyl)-5-[[4-(2-carboxyethyl)-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-4-(carboxymethyl)-5-(hydroxymethyl)-1H-pyrrol-3-yl]propanoic acid HMB Hydroxymethylbilane Preuroporphyrinogen C40H46N4O17 854.8098 854.285796066 3-(5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-(hydroxymethyl)-1H-pyrrol-2-yl]methyl}-2-{[4-(2-carboxyethyl)-5-{[4-(2-carboxyethyl)-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl}-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl)propanoic acid 3-(5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-(hydroxymethyl)-1H-pyrrol-2-yl]methyl}-2-{[4-(2-carboxyethyl)-5-{[4-(2-carboxyethyl)-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl}-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl)propanoic acid 73023-76-4 OCC1=C(CC(O)=O)C(CCC(O)=O)=C(CC2=C(CC(O)=O)C(CCC(O)=O)=C(CC3=C(CC(O)=O)C(CCC(O)=O)=C(CC4=C(CC(O)=O)C(CCC(O)=O)=CN4)N3)N2)N1 InChI=1S/C40H46N4O17/c45-17-32-25(12-40(60)61)21(4-8-36(52)53)29(44-32)15-31-24(11-39(58)59)20(3-7-35(50)51)28(43-31)14-30-23(10-38(56)57)19(2-6-34(48)49)27(42-30)13-26-22(9-37(54)55)18(16-41-26)1-5-33(46)47/h16,41-45H,1-15,17H2,(H,46,47)(H,48,49)(H,50,51)(H,52,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61) WDFJYRZCZIUBPR-UHFFFAOYSA-N Solid Cytosol logp 0.53 ALOGPS logs -4.42 ALOGPS solubility 3.23e-02 g/l ALOGPS logp 0.97 ChemAxon pka_strongest_acidic 3.25 ChemAxon iupac 3-(5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-(hydroxymethyl)-1H-pyrrol-2-yl]methyl}-2-{[4-(2-carboxyethyl)-5-{[4-(2-carboxyethyl)-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl}-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl)propanoic acid ChemAxon average_mass 854.8098 ChemAxon mono_mass 854.285796066 ChemAxon smiles OCC1=C(CC(O)=O)C(CCC(O)=O)=C(CC2=C(CC(O)=O)C(CCC(O)=O)=C(CC3=C(CC(O)=O)C(CCC(O)=O)=C(CC4=C(CC(O)=O)C(CCC(O)=O)=CN4)N3)N2)N1 ChemAxon formula C40H46N4O17 ChemAxon inchi InChI=1S/C40H46N4O17/c45-17-32-25(12-40(60)61)21(4-8-36(52)53)29(44-32)15-31-24(11-39(58)59)20(3-7-35(50)51)28(43-31)14-30-23(10-38(56)57)19(2-6-34(48)49)27(42-30)13-26-22(9-37(54)55)18(16-41-26)1-5-33(46)47/h16,41-45H,1-15,17H2,(H,46,47)(H,48,49)(H,50,51)(H,52,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61) ChemAxon inchikey WDFJYRZCZIUBPR-UHFFFAOYSA-N ChemAxon polar_surface_area 381.79 ChemAxon refractivity 209.92 ChemAxon polarizability 85.68 ChemAxon rotatable_bond_count 27 ChemAxon acceptor_count 17 ChemAxon donor_count 13 ChemAxon physiological_charge -8 ChemAxon formal_charge 0 ChemAxon Porphyrin and chlorophyll metabolism ec00860 Metabolic pathways eco01100 Porphyrin metabolism The metabolism of porphyrin begins with with glutamic acid being processed by an ATP-driven glutamyl-tRNA synthetase by interacting with hydrogen ion and tRNA(Glu), resulting in amo, pyrophosphate and L-glutamyl-tRNA(Glu) Glutamic acid. Glutamic acid can be obtained as a result of L-glutamate metabolism pathway, glutamate / aspartate : H+ symporter GltP, glutamate:sodium symporter or a glutamate / aspartate ABC transporter . L-glutamyl-tRNA(Glu) Glutamic acid interacts with a NADPH glutamyl-tRNA reductase resulting in a NADP, a tRNA(Glu) and a (S)-4-amino-5-oxopentanoate. This compound interacts with a glutamate-1-semialdehyde aminotransferase resulting a 5-aminolevulinic acid. This compound interacts with a porphobilinogen synthase resulting in a hydrogen ion, water and porphobilinogen. The latter compound interacts with water resulting in hydroxymethylbilane synthase resulting in ammonium, and hydroxymethylbilane. Hydroxymethylbilane can either be dehydrated to produce uroporphyrinogen I or interact with a uroporphyrinogen III synthase resulting in a water molecule and a uroporphyrinogen III. Uroporphyrinogen I interacts with hydrogen ion through a uroporphyrinogen decarboxylase resulting in a carbon dioxide and a coproporphyrinogen I Uroporphyrinogen III can be metabolized into precorrin by interacting with a S-adenosylmethionine through a siroheme synthase resulting in hydrogen ion, an s-adenosylhomocysteine and a precorrin-1. On the other hand, Uroporphyrinogen III interacts with hydrogen ion through a uroporphyrinogen decarboxylase resulting in a carbon dioxide and a Coproporphyrinogen III. Precorrin-1 reacts with a S-adenosylmethionine through a siroheme synthase resulting in a S-adenosylhomocysteine and a Precorrin-2. The latter compound is processed by a NAD dependent uroporphyrin III C-methyltransferase [multifunctional] resulting in a NADH and a sirohydrochlorin. This compound then interacts with Fe 2+ uroporphyrin III C-methyltransferase [multifunctional] resulting in a hydrogen ion and a siroheme. The siroheme is then processed in sulfur metabolism pathway. Uroporphyrinogen III can be processed in anaerobic or aerobic condition. Anaerobic: Uroporphyrinogen III interacts with an oxygen molecule, a hydrogen ion through a coproporphyrinogen III oxidase resulting in water, carbon dioxide and protoporphyrinogen IX. The latter compound then interacts with an 3 oxygen molecule through a protoporphyrinogen oxidase resulting in 3 hydrogen peroxide and a Protoporphyrin IX Aerobic: Uroporphyrinogen III reacts with S-adenosylmethionine through a coproporphyrinogen III dehydrogenase resulting in carbon dioxide, 5-deoxyadenosine, L-methionine and protoporphyrinogen IX. The latter compound interacts with a meanquinone through a protoporphyrinogen oxidase resulting in protoporphyrin IX. The protoporphyrin IX interacts with Fe 2+ through a ferrochelatase resulting in a hydrogen ion and a ferroheme b. The ferroheme b can either be incorporated into the oxidative phosphorylation as a cofactor of the enzymes involved in that pathway or it can interact with hydrogen peroxide through a catalase HPII resulting in a heme D. Heme D can then be incorporated into the oxidative phosphyrlation pathway as a cofactor of the enzymes involved in that pathway. Ferroheme b can also interact with water and a farnesyl pyrophosphate through a heme O synthase resulting in a release of pyrophosphate and heme O. Heme O is then incorporated into the Oxidative phosphorylation pathway. PW000936 Metabolic tetrapyrrole biosynthesis I PWY-5188 Specdb::EiMs 4970 Specdb::NmrOneD 275138 Specdb::NmrOneD 275139 Specdb::NmrOneD 275140 Specdb::NmrOneD 275141 Specdb::NmrOneD 275142 Specdb::NmrOneD 275143 Specdb::NmrOneD 275144 Specdb::NmrOneD 275145 Specdb::NmrOneD 275146 Specdb::NmrOneD 275147 Specdb::NmrOneD 275148 Specdb::NmrOneD 275149 Specdb::NmrOneD 275150 Specdb::NmrOneD 275151 Specdb::NmrOneD 275152 Specdb::NmrOneD 275153 Specdb::NmrOneD 275154 Specdb::NmrOneD 275155 Specdb::NmrOneD 275156 Specdb::NmrOneD 275157 Specdb::MsMs 21008 Specdb::MsMs 21009 Specdb::MsMs 21010 Specdb::MsMs 22559 Specdb::MsMs 22560 Specdb::MsMs 22561 Specdb::MsMs 2272143 Specdb::MsMs 2272144 Specdb::MsMs 2272145 Specdb::MsMs 3069462 Specdb::MsMs 3069463 Specdb::MsMs 3069464 HMDB01137 788 767 C01024 16645 HYDROXYMETHYLBILANE Hydroxymethylbilane 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 Porphobilinogen deaminase P06983 HEM3_ECOLI hemC http://ecmdb.ca/proteins/P06983.xml Uroporphyrinogen-III synthase P09126 HEM4_ECOLI hemD http://ecmdb.ca/proteins/P09126.xml Hydroxymethylbilane <> Water + Uroporphyrinogen III R03165 UROGENIIISYN-RXN Water + 4 Porphobilinogen > Hydroxymethylbilane +4 Ammonium 4 Porphobilinogen + Water <> Hydroxymethylbilane +4 Ammonia R00084 OHMETHYLBILANESYN-RXN Water + Porphobilinogen <> Hydrogen ion + Ammonia + Hydroxymethylbilane OHMETHYLBILANESYN-RXN 4 Porphobilinogen + Water > Hydroxymethylbilane +4 Ammonia R00084 OHMETHYLBILANESYN-RXN Hydroxymethylbilane > Uroporphyrinogen III + Water Hydroxymethylbilane <> Water + Uroporphyrinogen III 4 Porphobilinogen + Water <> Hydroxymethylbilane +4 Ammonia 4 Porphobilinogen + Water <> Hydroxymethylbilane +4 Ammonia