Updated BioCyc iOS App now
available in iTunes store
Updated BioCyc iOS App now
available in iTunes store
Updated BioCyc iOS App now
available in iTunes store
Updated BioCyc iOS App now
available in iTunes store
Updated BioCyc iOS App now
available in iTunes store

Escherichia coli K-12 substr. MG1655 Pathway: pyridoxal 5'-phosphate biosynthesis I
Inferred from experiment

Pathway diagram: 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:

Schematic showing all replicons, marked with selected genes

Genetic Regulation Schematic

Genetic regulation schematic for pyridoxal 5'-phosphate biosynthesis I

Synonyms: vitamin B6 biosynthesis

Superclasses: BiosynthesisCofactors, Prosthetic Groups, Electron Carriers BiosynthesisVitamins BiosynthesisVitamin B6 Biosynthesis

General Background

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. It is one of the most versatile cofactors that participates in transamination, decarboxylation, racemization, Cα-Cβ cleavage and α-β elimination reactions. This vitamin has a role in numerous human body functions ranging from modulation of hormone function to its recent discovery as a potent antioxidant. Its de novo biosynthesis occurs only in bacteria, fungi and plants, making it an essential nutrient in the human diet.

About This Pathway

The biosynthesis of this vitamin was thoroughly studied in E. 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.

An alternative and recently discovered DXP-independent pathway for PNP biosynthesis begins with glutamine in other micro-organisms and is very similar both structurally and mechanistically to the one in E. coli.

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

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

Variants: pyridoxal 5'-phosphate salvage I

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


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

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

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

Alefounder89: Alefounder PR, Perham RN (1989). "Identification, molecular cloning and sequence analysis of a gene cluster encoding the class II fructose 1,6-bisphosphate aldolase, 3-phosphoglycerate kinase and a putative second glyceraldehyde 3-phosphate dehydrogenase of Escherichia coli." Mol Microbiol 3(6);723-32. PMID: 2546007

Alper05: Alper H, Fischer C, Nevoigt E, Stephanopoulos G (2005). "Tuning genetic control through promoter engineering." Proc Natl Acad Sci U S A 102(36);12678-83. PMID: 16123130

Banks04: Banks J, Cane DE (2004). "Biosynthesis of vitamin B6: direct identification of the product of the PdxA-catalyzed oxidation of 4-hydroxy-l-threonine-4-phosphate using electrospray ionization mass spectrometry." Bioorg Med Chem Lett 14(7);1633-6. PMID: 15026039

Bartee15: Bartee D, Morris F, Al-Khouja A, Freel Meyers CL (2015). "Hydroxybenzaldoximes Are D-GAP-Competitive Inhibitors of E. coli 1-Deoxy-D-Xylulose-5-Phosphate Synthase." Chembiochem 16(12);1771-81. PMID: 26174207

Begley99: Begley TP, Downs DM, Ealick SE, McLafferty FW, Van Loon AP, Taylor S, Campobasso N, Chiu HJ, Kinsland C, Reddick JJ, Xi J (1999). "Thiamin biosynthesis in prokaryotes." Arch Microbiol 1999;171(5);293-300. PMID: 10382260

BoschiMuller97: Boschi-Muller S, Azza S, Pollastro D, Corbier C, Branlant G (1997). "Comparative enzymatic properties of GapB-encoded erythrose-4-phosphate dehydrogenase of Escherichia coli and phosphorylating glyceraldehyde-3-phosphate dehydrogenase." J Biol Chem 272(24);15106-12. PMID: 9182530

Brammer09: Brammer LA, Meyers CF (2009). "Revealing substrate promiscuity of 1-deoxy-D-xylulose 5-phosphate synthase." Org Lett 11(20);4748-51. PMID: 19778006

Brammer11: Brammer LA, Smith JM, Wade H, Meyers CF (2011). "1-Deoxy-D-xylulose 5-phosphate synthase catalyzes a novel random sequential mechanism." J Biol Chem 286(42);36522-31. PMID: 21878632

BRENDA14: BRENDA team (2014). Imported from BRENDA version existing on Aug 2014.

Campos01: Campos N, Rodriguez-Concepcion M, Seemann M, Rohmer M, Boronat A (2001). "Identification of gcpE as a novel gene of the 2-C-methyl-D-erythritol 4-phosphate pathway for isoprenoid biosynthesis in Escherichia coli." FEBS Lett 488(3);170-3. PMID: 11163766

Cane98: Cane DE, Hsiung Y, Cornish JA, Robinson JK, Spenser ID (1998). "Biosynthesis of Vitamin B6: The Oxidation of 4-(Phosphohydroxy)-L-threonine by PdxA." J Am Chem Soc 1998; 120:1936-1937.

Clarke73: Clarke SJ, Low B, Konigsberg WH (1973). "Close linkage of the genes serC (for phosphohydroxy pyruvate transaminase) and serS (for seryl-transfer ribonucleic acid synthetase) in Escherichia coli K-12." J Bacteriol 113(3);1091-5. PMID: 4570768

Di98: Di Salvo M, Yang E, Zhao G, Winkler ME, Schirch V (1998). "Expression, purification, and characterization of recombinant Escherichia coli pyridoxine 5'-phosphate oxidase." Protein Expr Purif 1998;13(3);349-56. PMID: 9693059

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

diSalvo03: di Salvo ML, Safo MK, Musayev FN, Bossa F, Schirch V (2003). "Structure and mechanism of Escherichia coli pyridoxine 5'-phosphate oxidase." Biochim Biophys Acta 1647(1-2);76-82. PMID: 12686112

Drewke96: Drewke C, Klein M, Clade D, Arenz A, Muller R, Leistner E (1996). "4-O-phosphoryl-L-threonine, a substrate of the pdxC(serC) gene product involved in vitamin B6 biosynthesis." FEBS Lett 1996;390(2);179-82. PMID: 8706854

Duncan86: Duncan K, Coggins JR (1986). "The serC-aro A operon of Escherichia coli. A mixed function operon encoding enzymes from two different amino acid biosynthetic pathways." Biochem J 1986;234(1);49-57. PMID: 3518706

Franco01: Franco MG, Laber B, Huber R, Clausen T (2001). "Structural basis for the function of pyridoxine 5'-phosphate synthase." Structure 9(3);245-53. PMID: 11286891

Garrido00: Garrido Franco M, Huber R, Schmidt FS, Laber B, Clausen T (2000). "Crystallization and preliminary X-ray crystallographic analysis of PdxJ, the pyridoxine 5'-phosphate synthesizing enzyme." Acta Crystallogr D Biol Crystallogr 2000;56 ( Pt 8);1045-8. PMID: 10944349

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Showing only 20 references. To show more, press the button "Show all references".

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.5 on Sat Apr 30, 2016, BIOCYC11A.