Journal
NATURE CHEMICAL BIOLOGY
Volume 13, Issue 3, Pages 290-+Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/NCHEMBIO.2273
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Funding
- European Commission [VITBIOMAL-012158]
- Deutsche Forschungsgemeinschaft (DFG) [TE368]
- NIH [DK44083]
- Robert A. Welch Foundation [A-0034]
- ESRF [Mx1461, Mx1732]
- RADDAM
- Diamond Light Source [Mx8891]
- University of Southampton
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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 the transfer of carbonyl-group-containing intermediates, despite their wide use in enzymatic catalysis. Here we show how imine chemistry operates in the transfer of covalent intermediates in pyridoxal 5'-phosphate biosynthesis by the Arabidopsis thaliana enzyme Pdx1. An initial ribose 5-phosphate lysine imine is converted to the chromophoric I-320 intermediate, simultaneously bound to two lysine residues and partially vacating the active site, which creates space for glyceraldehyde 3-phosphate to bind. Crystal structures show how substrate binding, catalysis and shuttling are coupled to conformational changes around strand beta(6) of the Pdx1 (beta alpha)(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 that follow a path of over 20 angstrom between substrate- and product-binding sites.
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