Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis

Abstract

Substrate channeling has emerged as a common mechanism for enzymatic intermediate transfer. A conspicuous gap in knowledge concerns the use of covalent lysine imines in transfer of carbonyl group-containing intermediates, despite their wide use in enzymatic catalysis. Here we show how imine chemistry operates in transfer of covalent intermediates in pyridoxal 5’-phosphate biosynthesis by the Arabidopsis enzyme Pdx1. An initial ribose 5-phosphate lysine imine converts to the chromophoric I320 intermediate, simultaneously bound to two lysine residues and partially vacating the active site, creating space for glyceraldehyde 3-phosphate to bind. Crystal structures show how substrate binding, catalysis and shuttling are coupled to conformational changes around strand ?6 of the Pdx1 (??)8-barrel. The dual specificity active site and imine relay mechanism for migration of carbonyl intermediates provide elegant solutions to the challenge of coordinating a complex sequence of reactions, following a path of over 20 Å between substrate and product binding sites.

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ORCID for Ivo Tews: orcid.org/0000-0002-4704-1139

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