Scientific article
Open access

Reaction mechanism of pyridoxal 5'-phosphate synthase: detection of an enzyme-bound chromophoric intermediate

Published inThe Journal of biological chemistry, vol. 282, no. 9, p. 6098-6105
Publication date2007

Vitamin B6 is an essential metabolite in all organisms. De novo synthesis of the vitamin can occur through either of two mutually exclusive pathways referred to as deoxyxylulose 5-phosphate-dependent and deoxyxylulose 5-phosphate-independent. The latter pathway has only recently been discovered and is distinguished by the presence of two genes, Pdx1 and Pdx2, encoding the synthase and glutaminase subunit of PLP synthase, respectively. In the presence of ammonia, the synthase alone displays an exceptional polymorphic synthetic ability in carrying out a complex set of reactions, including pentose and triose isomerization, imine formation, ammonia addition, aldol-type condensation, cyclization, and aromatization, that convert C3 and C5 precursors into the cofactor B6 vitamer, pyridoxal 5'-phosphate. Here, employing the Bacillus subtilis proteins, we demonstrate key features along the catalytic path. We show that ribose 5-phosphate is the preferred C5 substrate and provide unequivocal evidence that the pent(ul)ose phosphate imine occurs at lysine 81 rather than lysine 149 as previously postulated. While this study was under review, corroborative crystallographic evidence has been provided for imine formation with the corresponding lysine group in the enzyme from Thermotoga maritima (Zein, F., Zhang, Y., Kang, Y.-N., Burns, K., Begley, T. P., and Ealick, S. E. (2006) Biochemistry 45, 14609-14620). We have detected an unanticipated covalent reaction intermediate that occurs subsequent to imine formation and is dependent on the presence of Pdx2 and glutamine. This step most likely primes the enzyme for acceptance of the triose sugar, ultimately leading to formation of the pyridine ring. Two alternative structures are proposed for the chromophoric intermediate, both of which require substantial modifications of the proposed mechanism.

  • Bacillus subtilis/enzymology/metabolism
  • Bacterial Proteins
  • Glutaminase/metabolism
  • Glutamine
  • Ligases/metabolism
  • Protein Subunits
  • Ribosemonophosphates
  • Substrate Specificity
  • Trioses
  • Vitamin B 6/biosynthesis
Affiliation Not a UNIGE publication
Citation (ISO format)
RASCHLE, Thomas et al. Reaction mechanism of pyridoxal 5′-phosphate synthase: detection of an enzyme-bound chromophoric intermediate. In: The Journal of biological chemistry, 2007, vol. 282, n° 9, p. 6098–6105. doi: 10.1074/jbc.M610614200
Main files (1)
Article (Published version)
ISSN of the journal0021-9258

Technical informations

Creation11/24/2016 10:07:00 AM
First validation11/24/2016 10:07:00 AM
Update time03/15/2023 1:01:05 AM
Status update03/15/2023 1:01:04 AM
Last indexation01/16/2024 10:27:14 PM
All rights reserved by Archive ouverte UNIGE and the University of GenevaunigeBlack