Superpathway of pyridoxal 5'-phosphate biosynthesis and salvage (Solanum lycopersicum)

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10, 11, 13, 16, D-erythrose-4-phosphate 31erythronate-4-phosphate 2-oxo-3-hydroxy-4-phosphobutanoate 4-(phosphonooxy)-threonine (2S)-2-amino-3-oxo-4-phosphonooxybutanoate3-amino-1-hydroxyacetone 1-phosphateD-glyceraldehyde-3-phosphate 1-deoxy-D-xylulose 5-phosphate 1, 5, 22, 256pyridoxine-5'-phosphate 23, 26pyridoxal 5'-phosphate pyridoxal 2-4, 8, 9, 14...12, 26pyridoxine pyridoxamine 7pyridoxamine 5'-phosphate 21, 2.7.1.-


Pyridoxal 5'-phosphate (PLP) is the biochemically active form of pyridoxine 5'-phosphate (PNP)or vitamin B6. PLP is an essential cofactor of numerous metabolic enzymes, predominantly in amino acid metabolism


Synonyms: vitamin B6 biosynthesis and salvage / This superpathway shows the various ways that E. coli can obtain pyridoxal 5'-phosphate, a coenzyme for many enzymes that participate in amino acid and glycogen metabolism.
This pathway has been manually created based on Lycocyc content: Lyco: PWY0-845

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  1. Tomschy A, Glockshuber R, Jaenicke R; ''Functional expression of D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic eubacterium Thermotoga maritima in Escherichia coli. Authenticity and kinetic properties of the recombinant enzyme.''; Eur J Biochem, 1993 PubMed Europe PMC Scholia
  2. Gardiol A, Preiss J; ''Escherichia coli E-39 ADPglucose synthetase has different activation kinetics from the wild-type allosteric enzyme.''; Arch Biochem Biophys, 1990 PubMed Europe PMC Scholia
  3. Daub ME, Ehrenshaft M; ''THE PHOTOACTIVATED CERCOSPORA TOXIN CERCOSPORIN: Contributions to Plant Disease and Fundamental Biology.''; Annu Rev Phytopathol, 2000 PubMed Europe PMC Scholia
  4. Haghighi B, Flynn TG, Levy HR; ''Glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides. Isolation and sequence of a peptide containing an essential lysine.''; Biochemistry, 1982 PubMed Europe PMC Scholia
  5. Jankowski MD, Henry CS, Broadbelt LJ, Hatzimanikatis V; ''Group contribution method for thermodynamic analysis of complex metabolic networks.''; Biophys J, 2008 PubMed Europe PMC Scholia
  6. Herz S, Wungsintaweekul J, Schuhr CA, Hecht S, Luttgen H, Sagner S, Fellermeier M, Eisenreich W, Zenk MH, Bacher A, Rohdich F; ''Biosynthesis of terpenoids: YgbB protein converts 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate to 2C-methyl-D-erythritol 2,4-cyclodiphosphate.''; Proc Natl Acad Sci U S A, 2000 PubMed Europe PMC Scholia
  7. Mizote T, Nakayama H; ''Purification and properties of hydroxymethylpyrimidine kinase from Escherichia coli.''; Biochim Biophys Acta, 1989 PubMed Europe PMC Scholia
  8. John RA; ''Pyridoxal phosphate-dependent enzymes.''; Biochim Biophys Acta, 1995 PubMed Europe PMC Scholia
  9. Blumenthal KM, Smith EL; ''Nicotinamide adenine dinucleotide phosphate-specific glutamate dehydrogenase of Neurospora. I. Isolation, subunits, amino acid composition, sulfhydryl groups, and identification of a lysine residue reactive with pyridoxal phosphate and N-ethylmaleimide.''; J Biol Chem, 1973 PubMed Europe PMC Scholia
  10. Sivaraman J, Li Y, Banks J, Cane DE, Matte A, Cygler M; ''Crystal structure of Escherichia coli PdxA, an enzyme involved in the pyridoxal phosphate biosynthesis pathway.''; J Biol Chem, 2003 PubMed Europe PMC Scholia
  11. Yang Y, Zhao G, Winkler ME; ''Identification of the pdxK gene that encodes pyridoxine (vitamin B6) kinase in Escherichia coli K-12.''; FEMS Microbiol Lett, 1996 PubMed Europe PMC Scholia
  12. Furukawa Y, Yamada R, Iwashima A; ''Inactivation of microbial pyridoxal kinase by pyridoxal.''; Acta Vitaminol Enzymol, 1981 PubMed Europe PMC Scholia
  13. Yamada RH, Tsuji T, Nose Y; ''Uptake and utilization of vitamin B6 and its phosphate esters by Escherichia coli.''; J Nutr Sci Vitaminol (Tokyo), 1977 PubMed Europe PMC Scholia
  14. Breton J, Avanzi N, Magagnin S, Covini N, Magistrelli G, Cozzi L, Isacchi A; ''Functional characterization and mechanism of action of recombinant human kynurenine 3-hydroxylase.''; Eur J Biochem, 2000 PubMed Europe PMC Scholia
  15. Van Heyningen S, Shemin D; ''Inhibition of delta-aminolaevulate dehydratase by pyridoxal derivatives and by cyanide.''; Biochem J, 1971 PubMed Europe PMC Scholia
  16. Yang Y, Tsui HC, Man TK, Winkler ME; ''Identification and function of the pdxY gene, which encodes a novel pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate biosynthesis in Escherichia coli K-12.''; J Bacteriol, 1998 PubMed Europe PMC Scholia
  17. Braun M, L��nsdorf H, B��ckmann AF; ''12 alpha-hydroxysteroid dehydrogenase from Clostridium group P, strain C 48-50. Production, purification and characterization.''; Eur J Biochem, 1991 PubMed Europe PMC Scholia
  18. Aisaka K, Masuda T, Chikamune T, Kamitori K; ''Purification and characterization of trehalose phosphorylase from Catellatospora ferruginea.''; Biosci Biotechnol Biochem, 1998 PubMed Europe PMC Scholia
  19. Kaminskas E, Kimhi Y, Magasanik B; ''Urocanase and N-formimino-L-glutamate formiminohydrolase of Bacillus subtilis, two enzymes of the histidine degradation pathway.''; J Biol Chem, 1970 PubMed Europe PMC Scholia
  20. Emes AV, Hassall H; ''The degradation of L-histidine in the rat. The formation of imidazolylpyruvate, imidazolyl-lactate and imidazolylpropionate.''; Biochem J, 1973 PubMed Europe PMC Scholia
  21. Uyeda K, Rabinowitz JC; ''Enzymes of the clostridial purine fermentation. Serine hydroxymethyltransferase.''; Arch Biochem Biophys, 1968 PubMed Europe PMC Scholia
  22. Schryvers A, Lohmeier E, Weiner JH; ''Chemical and functional properties of the native and reconstituted forms of the membrane-bound, aerobic glycerol-3-phosphate dehydrogenase of Escherichia coli.''; J Biol Chem, 1978 PubMed Europe PMC Scholia
  23. Zhao G, Winkler ME; ''Kinetic limitation and cellular amount of pyridoxine (pyridoxamine) 5'-phosphate oxidase of Escherichia coli K-12.''; J Bacteriol, 1995 PubMed Europe PMC Scholia
  24. Miller AD, Packman LC, Hart GJ, Alefounder PR, Abell C, Battersby AR; ''Evidence that pyridoxal phosphate modification of lysine residues (Lys-55 and Lys-59) causes inactivation of hydroxymethylbilane synthase (porphobilinogen deaminase).''; Biochem J, 1989 PubMed Europe PMC Scholia
  25. Takahashi S, Abbe K, Yamada T; ''Purification of pyruvate formate-lyase from Streptococcus mutans and its regulatory properties.''; J Bacteriol, 1982 PubMed Europe PMC Scholia
  26. White RS, Dempsey WB; ''Purification and properties of vitamin B6 kinase from Escherichia coli B.''; Biochemistry, 1970 PubMed Europe PMC Scholia
  27. Golinelli-Pimpaneau B, Badet B; ''Possible involvement of Lys603 from Escherichia coli glucosamine-6-phosphate synthase in the binding of its substrate fructose 6-phosphate.''; Eur J Biochem, 1991 PubMed Europe PMC Scholia
  28. van der Meijden P, te Br��mmelstroet BW, Poirot CM, van der Drift C, Vogels GD; ''Purification and properties of methanol:5-hydroxybenzimidazolylcobamide methyltransferase from Methanosarcina barkeri.''; J Bacteriol, 1984 PubMed Europe PMC Scholia
  29. Yang Y, Zhao G, Man TK, Winkler ME; ''Involvement of the gapA- and epd (gapB)-encoded dehydrogenases in pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12.''; J Bacteriol, 1998 PubMed Europe PMC Scholia
  30. Figueroa CM, Esper MC, Bertolo A, Demonte AM, Aleanzi M, Iglesias AA, Ballicora MA; ''Understanding the allosteric trigger for the fructose-1,6-bisphosphate regulation of the ADP-glucose pyrophosphorylase from Escherichia coli.''; Biochimie, 2011 PubMed Europe PMC Scholia
  31. Crow VL, Wittenberger CL; ''Separation and properties of NAD+- and NADP+-dependent glyceraldehyde-3-phosphate dehydrogenases from Streptococcus mutans.''; J Biol Chem, 1979 PubMed Europe PMC Scholia
  32. Zhao G, Pease AJ, Bharani N, Winkler ME; ''Biochemical characterization of gapB-encoded erythrose 4-phosphate dehydrogenase of Escherichia coli K-12 and its possible role in pyridoxal 5'-phosphate biosynthesis.''; J Bacteriol, 1995 PubMed Europe PMC Scholia


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107271view14:36, 17 September 2019MaintBotChEBI identifier normalization
87608view08:54, 25 July 2016MirellaKalafatiOntology Term : 'classic metabolic pathway' added !
73656view17:41, 12 February 2014AndraChanged the layout to reflect the source
73655view16:41, 12 February 2014AndraAdded literature
73653view11:46, 12 February 2014AndraModified description
73652view11:41, 12 February 2014Andra
73648view23:48, 11 February 2014LarsEijssenNew pathway

External references


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NameTypeDatabase referenceComment
(2S)-2-amino-3-oxo-4-phosphonooxybutanoateMetabolite441260 (PubChem-compound)
1-deoxy-D-xylulose 5-phosphate MetaboliteCHEBI:16493 (ChEBI) (Enzyme Nomenclature) GeneProduct1.1.1.290 (Enzyme Nomenclature) GeneProduct1.2.1.72 (Enzyme Nomenclature) GeneProduct1.4.3.5 (Enzyme Nomenclature)
2-oxo-3-hydroxy-4-phosphobutanoate MetaboliteCHEBI:27951 (ChEBI) GeneProduct2.2.1.7 (Enzyme Nomenclature) GeneProduct2.6.1.52 (Enzyme Nomenclature) GeneProduct2.6.99.2 (Enzyme Nomenclature)
2.7.1.- GeneProduct2.7.1.- (Enzyme Nomenclature) GeneProduct2.7.1.35 (Enzyme Nomenclature)
3-amino-1-hydroxyacetone 1-phosphateMetaboliteCHEBI:1449 (ChEBI)
4-(phosphonooxy)-threonine MetaboliteCHEBI:18336 (ChEBI)
D-erythrose-4-phosphate MetaboliteCHEBI:48153 (ChEBI)
D-glyceraldehyde-3-phosphate MetaboliteCHEBI:17138 (ChEBI)
erythronate-4-phosphate MetaboliteCHEBI:49003 (ChEBI)
pyridoxal 5'-phosphate MetaboliteCHEBI:18405 (ChEBI)
pyridoxal MetaboliteCHEBI:17310 (ChEBI)
pyridoxamine 5'-phosphate MetaboliteCHEBI:18335 (ChEBI)
pyridoxamine MetaboliteCHEBI:16410 (ChEBI)
pyridoxine MetaboliteCHEBI:16709 (ChEBI)
pyridoxine-5'-phosphate MetaboliteCHEBI:28803 (ChEBI)

Annotated Interactions

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