13C NMR snapshots of the complex reaction coordinate of pyridoxal phosphate synthase

Nat Chem Biol. 2008 Jul;4(7):425-30. doi: 10.1038/nchembio.93. Epub 2008 May 30.

Abstract

The predominant biosynthetic route to vitamin B6 is catalyzed by a single enzyme. The synthase subunit of this enzyme, Pdx1, operates in concert with the glutaminase subunit, Pdx2, to catalyze the complex condensation of ribose 5-phosphate, glutamine and glyceraldehyde 3-phosphate to form pyridoxal 5'-phosphate, the active form of vitamin B6. In previous studies it became clear that many if not all of the reaction intermediates were covalently bound to the synthase subunit, thus making them difficult to isolate and characterize. Here we show that it is possible to follow a single turnover reaction by heteronuclear NMR using (13)C- and (15)N-labeled substrates as well as (15)N-labeled synthase. By denaturing the enzyme at points along the reaction coordinate, we solved the structures of three covalently bound intermediates. This analysis revealed a new 1,5 migration of the lysine amine linking the intermediate to the enzyme during the conversion of ribose 5-phosphate to pyridoxal 5'-phosphate.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Bacillus subtilis / enzymology*
  • Bacillus subtilis / metabolism
  • Carbon Isotopes
  • Catalysis
  • Glutaminase / chemistry
  • Glutaminase / isolation & purification
  • Glutaminase / metabolism*
  • Kinetics
  • Nuclear Magnetic Resonance, Biomolecular
  • Pyridoxal Phosphate / biosynthesis*
  • Pyridoxal Phosphate / chemistry
  • Ribosemonophosphates / chemistry
  • Ribosemonophosphates / isolation & purification
  • Ribosemonophosphates / metabolism*
  • Substrate Specificity
  • Vitamin B 6 / biosynthesis*
  • Vitamin B 6 / chemistry

Substances

  • Carbon Isotopes
  • Ribosemonophosphates
  • ribose-5-phosphate
  • Pyridoxal Phosphate
  • Vitamin B 6
  • Glutaminase

Associated data

  • PubChem-Substance/49737753
  • PubChem-Substance/49737754
  • PubChem-Substance/49737755
  • PubChem-Substance/49737756
  • PubChem-Substance/49737757
  • PubChem-Substance/49737758
  • PubChem-Substance/49737759
  • PubChem-Substance/49737760
  • PubChem-Substance/49737761
  • PubChem-Substance/49737762
  • PubChem-Substance/49737763
  • PubChem-Substance/49737764
  • PubChem-Substance/49737765
  • PubChem-Substance/49737766
  • PubChem-Substance/49737767
  • PubChem-Substance/49737768
  • PubChem-Substance/49737769
  • PubChem-Substance/49737770
  • PubChem-Substance/49737771
  • PubChem-Substance/49737772
  • PubChem-Substance/49737773
  • PubChem-Substance/49737774