Pyridoxal phosphate (active vitamin B6) biosynthesis PdxJ (IPR004569)

Short name: PyrdxlP_synth_PdxJ

Overlapping homologous superfamilies

Family relationships



Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). Pyridoxal 5'-phosphate (PLP) is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination [PMID: 8690703, PMID: 7748903, PMID: 15189147]. PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors [PMID: 17109392]. Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy [PMID: 16763894].

PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalysed reactions, enzymatic and non-enzymatic [PMID: 15581583].

In Escherichia coli, the pdx genes involved in vitamin B6 have been characterised [PMID: 10225425, PMID: 15242009, PMID: 17344055]. This entry represents PdxJ (also called PNP synthase), which catalyses the condensation of 4-hydroxy-L-threonine and 1-deoxy-D-xylulose-5-phosphate to form pyridoxine-5'-phosphate (PNP) [PMID: 10225425]. The product of the PdxJ reaction is then oxidized by PdxH to form pyridoxal 5'-phosphate (PLP).

PNP synthase (PdxJ) adopts a TIM barrel topology. Intersubunit contacts are mediated by three ''extra'' helices, generating a tetramer of symmetric dimers with shared active sites. The open state has been proposed to accept substrates and to release products, while most of the catalytic events are likely to occur in the closed state. A hydrophilic channel running through the centre of the barrel was identified as the essential structural feature that enables PNP synthase to release water molecules produced during the reaction from the closed, solvent-shielded active site [PMID: 11286891].

GO terms

Biological Process

GO:0008615 pyridoxine biosynthetic process

Molecular Function

GO:0033856 pyridoxine 5'-phosphate synthase activity

Cellular Component

GO:0005737 cytoplasm

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.