2.0 2012-05-31 13:47:50 -0600 2015-06-03 15:53:51 -0600 ECMDB01213 M2MDB000301 1-Deoxy-D-xylulose 5-phosphate 1-Deoxy-D-xylulose 5-phosphate is an intermediate in the non-mevalonate pathway. This is an alternative metabolic pathway leading to the formation of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). The key enzyme in the non-mevalonate pathway of isoprenoid biosynthesis is 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR). 1-Deoxy-D-threo-pentulose 5-phosphate 1-Deoxy-D-threo-pentulose 5-phosphoric acid 1-Deoxy-D-xylulose 5-phosphate 1-Deoxy-D-xylulose 5-phosphoric acid 1DX5P D-1-Deoxyxylulose-5-P Deoxyxylulose-5-phosphate Deoxyxylulose-5-phosphoric acid DOXP DXP C5H11O7P 214.1104 214.024239218 {[(2R,3S)-2,3-dihydroxy-4-oxopentyl]oxy}phosphonic acid 1-deoxy-D-xylulose-5-phosphate 190079-18-6 CC(=O)[C@@H](O)[C@H](O)COP(O)(O)=O InChI=1S/C5H11O7P/c1-3(6)5(8)4(7)2-12-13(9,10)11/h4-5,7-8H,2H2,1H3,(H2,9,10,11)/t4-,5-/m1/s1 AJPADPZSRRUGHI-RFZPGFLSSA-N Solid Cytosol logp -1.93 ALOGPS logs -0.89 ALOGPS solubility 2.76e+01 g/l ALOGPS logp -1.9 ChemAxon pka_strongest_acidic 1.48 ChemAxon pka_strongest_basic -3.6 ChemAxon iupac {[(2R,3S)-2,3-dihydroxy-4-oxopentyl]oxy}phosphonic acid ChemAxon average_mass 214.1104 ChemAxon mono_mass 214.024239218 ChemAxon smiles CC(=O)[C@@H](O)[C@H](O)COP(O)(O)=O ChemAxon formula C5H11O7P ChemAxon inchi InChI=1S/C5H11O7P/c1-3(6)5(8)4(7)2-12-13(9,10)11/h4-5,7-8H,2H2,1H3,(H2,9,10,11)/t4-,5-/m1/s1 ChemAxon inchikey AJPADPZSRRUGHI-RFZPGFLSSA-N ChemAxon polar_surface_area 124.29 ChemAxon refractivity 40.77 ChemAxon polarizability 17.18 ChemAxon rotatable_bond_count 5 ChemAxon acceptor_count 6 ChemAxon donor_count 4 ChemAxon physiological_charge -2 ChemAxon formal_charge 0 ChemAxon Vitamin B6 metabolism ec00750 Thiamine metabolism ec00730 Terpenoid backbone biosynthesis ec00900 Metabolic pathways eco01100 Secondary metabolites: isoprenoid biosynthesis (nonmevalonate pathway) The biosynthesis of isoprenoids starts with a D-glyceraldehyde 3-phosphate interacting with a hydrogen ion through a 1-deoxyxylulose-5-phosphate synthase resulting in a carbon dioxide and 1-Deoxy-D-xylulose. The latter compound then interacts with a hydrogen ion through a NADPH driven 1-deoxy-D-xylulose 5-phosphate reductoisomerase resulting in a NADP and a 2-C-methyl-D-erythritol 4-phosphate. The latter compound then interacts with a cytidine triphosphate and a hydrogen ion through a 4-diphosphocytidyl-2C-methyl-D-erythritol synthase resulting in a pyrophosphate and a 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol. The latter compound is then phosphorylated through an ATP driven 4-diphosphocytidyl-2-C-methylerythritol kinase resulting in a release of an ADP, a hydrogen ion and a 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol. The latter compound then interacts with a 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase resulting in the release of a 2-C-methyl-D-erythritol-2,4-cyclodiphosphate resulting in the release of a cytidine monophosphate and 2-C-methyl-D-erythritol-2,4-cyclodiphosphate. The latter compound then interacts with a reduced flavodoxin through a 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase resulting in the release of a water molecule, a hydrogen ion, an oxidized flavodoxin and a 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate. The compound 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate can interact with an NADPH,a hydrogen ion through a 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase resulting in a NADP, a water molecule and either a Dimethylallylpyrophosphate or a Isopentenyl pyrophosphate. These two last compounds can be are isomers that can be produced through a isopentenyl diphosphate isomerase.and then get incorporated into the methylerythritol phosphate and polyisoprenoid biosynthesis pathway PW000975 Metabolic Secondary metabolites: methylerythritol phosphate and polyisoprenoid biosynthesis The biosynthesis of isoprenoids starts with a D-glyceraldehyde 3-phosphate interacting with a hydrogen ion through a 1-deoxyxylulose-5-phosphate synthase resulting in a carbon dioxide and 1-Deoxy-D-xylulose. The latter compound then interacts with a hydrogen ion through a NADPH driven 1-deoxy-D-xylulose 5-phosphate reductoisomerase resulting in a NADP and a 2-C-methyl-D-erythritol 4-phosphate. The latter compound then interacts with a cytidine triphosphate and a hydrogen ion through a 4-diphosphocytidyl-2C-methyl-D-erythritol synthase resulting in a pyrophosphate and a 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol. The latter compound is then phosphorylated through an ATP driven 4-diphosphocytidyl-2-C-methylerythritol kinase resulting in a release of an ADP, a hydrogen ion and a 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol. The latter compound then interacts with a 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase resulting in the release of a 2-C-methyl-D-erythritol-2,4-cyclodiphosphate resulting in the release of a cytidine monophosphate and 2-C-methyl-D-erythritol-2,4-cyclodiphosphate. The latter compound then interacts with a reduced flavodoxin through a 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase resulting in the release of a water molecule, a hydrogen ion, an oxidized flavodoxin and a 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate. The compound 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate can interact with an NADPH,a hydrogen ion through a 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase resulting in a NADP, a water molecule and either a Dimethylallylpyrophosphate or a Isopentenyl pyrophosphate. These two last compounds can be are isomers that can be produced through a isopentenyl diphosphate isomerase. Dimethylallylpyrophosphate interacts with the isopentenyl pyrophosphate through a geranyl diphosphate synthase / farnesyl diphosphate synthase resulting in a pyrophosphate and a geranyl--PP. The latter compound interacts with a Isopentenyl pyrophosphate through a geranyl diphosphate synthase / farnesyl diphosphate synthase resulting in the release of a pyrophosphate and a farnesyl pyrophosphate. The latter compound interacts with isopentenyl pyrophosphate either through a undecaprenyl diphosphate synthase resulting in a release of a pyrophosphate and a di-trans,octa-cis-undecaprenyl diphosphate or through a octaprenyl diphosphate synthase resulting in a pyrophosphate and an octaprenyl diphosphate PW000958 Metabolic Vitamin B6 1430936196 PW000891 Metabolic Thiazole Biosynthesis I This pathway describes only the synthesis of the thiazole moiety of thiamin. Different variations of this pathway exist, this particular pathway describes the pathway that occurs in Escherichia coli K-12 and Salmonella enterica enterica serovar Typhimurium. The biosynthesis of the thiazole moiety is complex. In Escherichia coli it involves six proteins, the products of the thiS, thiF, thiG, thiH, thiI, and iscS genes. The process begins when IscS, a protein that is also involved in the biosynthesis of iron-sulfur clusters, catalyzes the transfer of a sulfur atom from cysteine to a ThiI sulfur-carrier protein, generating a an S-sulfanyl-[ThiI sulfur-carrier protein]. In a parallel route, the ThiF protein activates a ThiS sulfur-carrier protein by adenylation of its carboxy terminus, generating a carboxy-adenylated-[ThiS sulfur-carrier protein]. In a second reaction, which may also be catalyzed by ThiF, the sulfur from an S-sulfanyl-[ThiI sulfur-carrier protein] is transferred to ThiS, generating a thiocarboxy-[ThiS-Protein]. The final reaction of this pathway, which is catalyzed by the ThiG protein, requires three inputs: a thiocarboxy-[ThiS-Protein], 1-deoxy-D-xylulose 5-phosphate and 2-iminoacetate. 2-iminoacetate is formed in Escherichia coli from L-tyrosine by tyrosine lyase (ThiH), which forms a complex with ThiG. For many years the products of this reaction was assumed to be 4-methyl-5-(β-hydroxyethyl)thiazole (thiazole). However, recent work performed with the thiazole synthase from Bacillus subtilis has shown that the actual product is the thiazole tautomer 2-[(2R,5Z)-(2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate. While in Bacillus a dedicated thiazole tautomerase converts this product into a different tautomer (2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate), most of the proteobacteria lack the tautomerase. (EcoCyc) PW002041 Metabolic thiazole biosynthesis I (E. coli) PWY-6892 methylerythritol phosphate pathway NONMEVIPP-PWY pyridoxal 5'-phosphate biosynthesis I PYRIDOXSYN-PWY Specdb::CMs 3178 Specdb::CMs 37978 Specdb::CMs 165946 Specdb::NmrOneD 87552 Specdb::NmrOneD 87553 Specdb::NmrOneD 87554 Specdb::NmrOneD 87555 Specdb::NmrOneD 87556 Specdb::NmrOneD 87557 Specdb::NmrOneD 87558 Specdb::NmrOneD 87559 Specdb::NmrOneD 87560 Specdb::NmrOneD 87561 Specdb::NmrOneD 87562 Specdb::NmrOneD 87563 Specdb::NmrOneD 87564 Specdb::NmrOneD 87565 Specdb::NmrOneD 87566 Specdb::NmrOneD 87567 Specdb::NmrOneD 87568 Specdb::NmrOneD 87569 Specdb::NmrOneD 87570 Specdb::NmrOneD 87571 Specdb::MsMs 23219 Specdb::MsMs 23220 Specdb::MsMs 23221 Specdb::MsMs 30017 Specdb::MsMs 30018 Specdb::MsMs 30019 Specdb::MsMs 1471391 Specdb::MsMs 1471392 Specdb::MsMs 1471393 Specdb::MsMs 1471394 Specdb::MsMs 1471395 Specdb::MsMs 1471396 Specdb::MsMs 1471397 Specdb::MsMs 1471398 Specdb::MsMs 1471399 Specdb::MsMs 1471400 Specdb::MsMs 1471401 Specdb::MsMs 1471402 Specdb::MsMs 1471403 Specdb::MsMs 1471404 Specdb::MsMs 1471405 Specdb::MsMs 1471406 Specdb::MsMs 1471407 Specdb::MsMs 1471408 Specdb::MsMs 1471409 HMDB01213 443201 391473 C11437 16493 DEOXYXYLULOSE-5P DXP 1-Deoxy-D-xylulose 5-phosphate 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 Blagg, Brian S. J.; Poulter, C. Dale. Synthesis of 1-Deoxy-D-xylulose and 1-Deoxy-D-xylulose-5-phosphate. Journal of Organic Chemistry (1999), 64(5), 1508-1511. Xylulose kinase P09099 XYLB_ECOLI xylB http://ecmdb.ca/proteins/P09099.xml Cysteine desulfurase P0A6B7 ISCS_ECOLI iscS http://ecmdb.ca/proteins/P0A6B7.xml Pyridoxine 5'-phosphate synthase P0A794 PDXJ_ECOLI pdxJ http://ecmdb.ca/proteins/P0A794.xml 4-hydroxythreonine-4-phosphate dehydrogenase P19624 PDXA_ECOLI pdxA http://ecmdb.ca/proteins/P19624.xml 1-deoxy-D-xylulose 5-phosphate reductoisomerase P45568 DXR_ECOLI dxr http://ecmdb.ca/proteins/P45568.xml 1-deoxy-D-xylulose-5-phosphate synthase P77488 DXS_ECOLI dxs http://ecmdb.ca/proteins/P77488.xml Sulfur carrier protein ThiS adenylyltransferase P30138 THIF_ECOLI thiF http://ecmdb.ca/proteins/P30138.xml tRNA sulfurtransferase P77718 THII_ECOLI thiI http://ecmdb.ca/proteins/P77718.xml Thiazole synthase P30139 THIG_ECOLI thiG http://ecmdb.ca/proteins/P30139.xml Sulfur carrier protein ThiS O32583 THIS_ECOLI thiS http://ecmdb.ca/proteins/O32583.xml Dehydroglycine synthase P30140 THIH_ECOLI thiH http://ecmdb.ca/proteins/P30140.xml 1-Deoxy-D-xylulose 5-phosphate + NAD + O-Phospho-4-hydroxy-L-threonine > Carbon dioxide + Hydrogen ion +2 Water + NADH + Pyridoxine 5'-phosphate + Phosphate Adenosine triphosphate + Dehydroglycine + 1-Deoxy-D-xylulose 5-phosphate + Hydrogen ion + IscS with bound sulfur + NADPH > 4-Methyl-5-(2-phosphoethyl)-thiazole + Adenosine monophosphate + Carbon dioxide +2 Water + IscS sulfur acceptor protein + NADP + Pyrophosphate 1-Deoxy-D-xylulose 5-phosphate + Hydrogen ion + NADPH <> 2-C-Methyl-D-erythritol-4-phosphate + NADP R05688 DXPREDISOM-RXN D-Glyceraldehyde 3-phosphate + Hydrogen ion + Pyruvic acid <> Carbon dioxide + 1-Deoxy-D-xylulose 5-phosphate R05636 DXS-RXN Adenosine triphosphate + 1-Deoxy-D-xylulose > ADP + 1-Deoxy-D-xylulose 5-phosphate + Hydrogen ion RXN0-382 Pyruvic acid + D-Glyceraldehyde 3-phosphate <> 1-Deoxy-D-xylulose 5-phosphate + Carbon dioxide R05636 DXS-RXN 2-C-Methyl-D-erythritol-4-phosphate + NADP <> 1-Deoxy-D-xylulose 5-phosphate + NADPH + Hydrogen ion R05688 DXPREDISOM-RXN 3-Amino-2-oxopropyl phosphate + 1-Deoxy-D-xylulose 5-phosphate + 3-Amino-2-oxopropyl phosphate <> Pyridoxine 5'-phosphate + Phosphate +2 Water R05838 Pyruvic acid + D-Glyceraldehyde 3-phosphate + Hydrogen ion > Carbon dioxide + 1-Deoxy-D-xylulose 5-phosphate DXS-RXN 1-Amino-propan-2-one-3-phosphate + 1-Deoxy-D-xylulose 5-phosphate > Hydrogen ion + Pyridoxine 5'-phosphate + Phosphate + Water PDXJ-RXN 2-C-methyl-D-erythritol 4-phosphate + NADP > 1-Deoxy-D-xylulose 5-phosphate + NADPH Pyruvic acid + D-Glyceraldehyde 3-phosphate > 1-Deoxy-D-xylulose 5-phosphate + Carbon dioxide 1-Deoxy-D-xylulose 5-phosphate + 2-Amino-3-phosphonopropionic acid > Pyridoxine 5'-phosphate + Inorganic phosphate +2 Water 1-Deoxy-D-xylulose 5-phosphate + 2-iminoacetate + thiocarboxy-adenylate-[sulfur-carrier protein ThiS] > 2-((2R,5Z)-2-Carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate + [sulfur-carrier protein ThiS] +2 Water 1-Deoxy-D-xylulose 5-phosphate + 2-iminoacetate <> 2-[(2R,5Z)-2-Carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate +2 Water R10247 1-Deoxy-D-xylulose 5-phosphate + 2-Amino-3-phosphonopropionic acid + 1-Deoxy-D-xylulose 5-phosphate + 2-Amino-3-phosphonopropionic acid > Pyridoxine 5'-phosphate + Phosphate + Hydrogen ion +2 Water PW_R003329 D-Glyceraldehyde 3-phosphate + Pyruvic acid + Hydrogen ion + D-Glyceraldehyde 3-phosphate > 1-Deoxy-D-xylulose 5-phosphate + Carbon dioxide + 1-Deoxy-D-xylulose 5-phosphate PW_R003330 D-Glyceraldehyde 3-phosphate + Hydrogen ion + D-Glyceraldehyde 3-phosphate > Carbon dioxide + 1-Deoxy-D-xylulose 5-phosphate + 1-Deoxy-D-xylulose 5-phosphate PW_R003687 NADPH + Hydrogen ion + 1-Deoxy-D-xylulose 5-phosphate + NADPH + 1-Deoxy-D-xylulose 5-phosphate > NADP + 2-C-methyl-D-erythritol 4-phosphate PW_R003688 1-Deoxy-D-xylulose 5-phosphate + Dehydroglycine + a thiocarboxy-[ThiS-Protein] > 2-((2R,5Z)-2-Carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate + a ThiS sulfur-carrier protein +2 Water PW_R005964 1-Deoxy-D-xylulose 5-phosphate + 2 2-iminoacetate <>2 2-[(2R,5Z)-2-Carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate +2 Water 3 3-Amino-2-oxopropyl phosphate + 1-Deoxy-D-xylulose 5-phosphate <> Pyridoxine 5'-phosphate + Phosphate +2 Water 1-Deoxy-D-xylulose 5-phosphate + Hydrogen ion + NADPH <>2 2-C-Methyl-D-erythritol-4-phosphate + NADP D-Glyceraldehyde 3-phosphate + Hydrogen ion + Pyruvic acid <> Carbon dioxide + 1-Deoxy-D-xylulose 5-phosphate Pyruvic acid + D-Glyceraldehyde 3-phosphate <> 1-Deoxy-D-xylulose 5-phosphate + Carbon dioxide 1-Deoxy-D-xylulose 5-phosphate + Hydrogen ion + NADPH <>2 2-C-Methyl-D-erythritol-4-phosphate + NADP D-Glyceraldehyde 3-phosphate + Hydrogen ion + Pyruvic acid <> Carbon dioxide + 1-Deoxy-D-xylulose 5-phosphate