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Caulobacter crescentus CB15 Pathway: pyridoxal 5'-phosphate biosynthesis I

If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Locations of Mapped Genes:

Synonyms: vitamin B6 biosynthesis

Superclasses: Biosynthesis Cofactors, Prosthetic Groups, Electron Carriers Biosynthesis Vitamins Biosynthesis Vitamin B6 Biosynthesis

Pathway Summary from MetaCyc:
General Background

Vitamin B6 is a group term for pyridoxal (PL), pyridoxine (PN), pyridoxamine (PM) and their 5'-phosphorylated derivatives pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate (PNP) and pyridoxamine 5'-phosphate (PMP), which are also referred to as vitamers. Pyridoxal 5'-phosphate (PLP) is the biochemically active form, and is an essential cofactor in all living systems [John95]. It plays an important role in amino acid and carbohydrate metabolism and has recently been implicated in singlet oxygen resistance [Daub00]. Most bacteria, archaebacteria, fungi, and plants synthesize PLP in a single reaction, as described in pyridoxal 5'-phosphate biosynthesis II, although some bacteria, such as Escherichia coli, use a longer, more complex pathway (pyridoxal 5'-phosphate biosynthesis I) [Yang98, Sivaraman03]. Animals do not synthesize this compound, making it an essential nutrient in their diet.

PLP is an essential cofactor of numerous metabolic enzymes, predominantly in amino acid metabolism. It is one of the most versatile cofactors and participates in transamination, decarboxylation, racemization, Cα-Cβ cleavage and α-β elimination reactions. In humans this vitamin has a role in numerous functions ranging from modulation of hormone function to potent antioxidant activity.

About This Pathway

The biosynthesis of this vitamin was thoroughly studied in Escherichia coli and involves two branches with seven enzymatic steps. In one branch, the sequential action of the enzymes Epd, PdxB and SerC results in the convesrion of erythrose 4-phosphate into 4-phosphohydroxy-L-threonine. The latter then undergoes oxidation and decarboxylation by PdxA to form 3-hydroxy-1-aminoacetone phosphate. In the other branch, deoxyxylulose 5-phosphate (DXP) is derived from glyceraldehyde 3-phosphate (GAP) and pyruvate by the action of Dxs. The products of the two branches, i.e. 3-hydroxy-1-aminoacetone phosphate and DXP, are then condensed by PdxJ to form PNP, which enters the salvage pathway to undergo oxidation by PdxH to form the PLP cofactor.

From the six pdx genes, two of them, epd and serC, are involved in other metabolic processes, but pdxA, pdxB, pdxJ and pdxH are unique for PLP biosynthesis [Lam92]. PdxJ, the PNP synthase is the key ezyme that catalyzes a multistep ring closure yielding PNP and inorganic phosphate (Pi). This is the last step in the de novo synthetic pathway.

This topic has been reviewed in [Fitzpatrick07, Sakai04, GarridoFranco03].

An alternative DXP-independent pathway for PNP biosynthesis is described at pyridoxal 5'-phosphate biosynthesis II.

Superpathways: superpathway of pyridoxal 5'-phosphate biosynthesis and salvage

Variants: pyridoxal 5'-phosphate salvage I

Pathway Evidence Glyph:

Key to pathway glyph edge colors: ?

  An enzyme catalyzing this reaction is present in this organism
  No enzyme catalyzing this reaction has been identified in this organism
  The reaction and any enzyme that catalyzes it (if one has been identified) is unique to this pathway
  Represents spontaneous reactions, or lines that do not represent reactions (e.g. in polymerization pathways)

Created 18-Jan-1996 by Riley M , Marine Biological Laboratory
Reviewed 15-Mar-2010 by Sarker M , SRI International


Daub00: Daub ME, Ehrenshaft M (2000). "THE PHOTOACTIVATED CERCOSPORA TOXIN CERCOSPORIN: Contributions to Plant Disease and Fundamental Biology." Annu Rev Phytopathol 38;461-490. PMID: 11701851

Fitzpatrick07: Fitzpatrick TB, Amrhein N, Kappes B, Macheroux P, Tews I, Raschle T (2007). "Two independent routes of de novo vitamin B6 biosynthesis: not that different after all." Biochem J 407(1);1-13. PMID: 17822383

GarridoFranco03: Garrido-Franco M (2003). "Pyridoxine 5'-phosphate synthase: de novo synthesis of vitamin B6 and beyond." Biochim Biophys Acta 1647(1-2);92-7. PMID: 12686115

John95: John RA (1995). "Pyridoxal phosphate-dependent enzymes." Biochim Biophys Acta 1248(2);81-96. PMID: 7748903

Lam92: Lam HM, Tancula E, Dempsey WB, Winkler ME (1992). "Suppression of insertions in the complex pdxJ operon of Escherichia coli K-12 by lon and other mutations." J Bacteriol 1992;174(5);1554-67. PMID: 1537800

Sakai04: Sakai A, Kita M, Tani Y (2004). "Recent progress of vitamin B6 biosynthesis." J Nutr Sci Vitaminol (Tokyo) 50(2);69-77. PMID: 15242009

Sivaraman03: Sivaraman J, Li Y, Banks J, Cane DE, Matte A, Cygler M (2003). "Crystal structure of Escherichia coli PdxA, an enzyme involved in the pyridoxal phosphate biosynthesis pathway." J Biol Chem 278(44);43682-90. PMID: 12896974

Yang98: Yang Y, Zhao G, Man TK, Winkler ME (1998). "Involvement of the gapA- and epd (gapB)-encoded dehydrogenases in pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12." J Bacteriol 1998;180(16);4294-9. PMID: 9696782

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Herz00a: Herz S, Wungsintaweekul J, Schuhr CA, Hecht S, Luttgen H, Sagner S, Fellermeier M, Eisenreich W, Zenk MH, Bacher A, Rohdich F (2000). "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 97(6);2486-90. PMID: 10694574

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