title: 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 the transfer of carbonyl-group-containing intermediates, despite their wideuse 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 I320intermediate, 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 β6 of the Pdx1 (βα)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 Å between substrate- and product-binding sites.
authors.affiliation: Biological Sciences, University of Southampton, Southampton, UK.|Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Rodrigues
authors.affiliation: Biological Sciences, University of Southampton, Southampton, UK.|Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.
authors.forename: Volker
authors.initials: V
authors.lastname: Windeisen
authors.affiliation: Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.
authors.forename: Gabriela
authors.initials: G
authors.lastname: Guédez
authors.affiliation: Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Weber
authors.affiliation: Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.
authors.forename: Marco
authors.initials: M
authors.lastname: Strohmeier
authors.affiliation: Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA.|Pacific Biosciences, Menlo Park, California, USA.
authors.forename: Jeremiah W
authors.initials: JW
authors.lastname: Hanes
authors.affiliation: Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France.|European Synchrotron Radiation Facility, Grenoble, France.
authors.forename: Antoine
authors.initials: A
authors.lastname: Royant
authors.affiliation: Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
authors.forename: Gwyndaf
authors.identifier: 0000-0002-6079-2201
authors.initials: G
authors.lastname: Evans
authors.affiliation: Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.
authors.forename: Irmgard
authors.initials: I
authors.lastname: Sinning
authors.affiliation: Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA.
authors.forename: Steven E
authors.initials: SE
authors.lastname: Ealick
authors.affiliation: Department of Chemistry, Texas A&M University, College Station, Texas, USA.
authors.forename: Tadhg P
authors.initials: TP
authors.lastname: Begley
authors.affiliation: Biological Sciences, University of Southampton, Southampton, UK.|Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.
authors.forename: Ivo
authors.identifier: 0000-0002-4704-1139
authors.initials: I
authors.lastname: Tews
mesh_terms: D029681:Arabidopsis Proteins / Q000737:chemistry / Q000378:metabolism; D019759:Carbon-Nitrogen Lyases; D008239:Lysine / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D015394:Molecular Structure; D019884:Nitrogenous Group Transferases / Q000737:chemistry / Q000378:metabolism; D025101:Vitamin B 6 / Q000096:biosynthesis* / Q000737:chemistry
chemical_list: D029681:Arabidopsis Proteins; D025101:Vitamin B 6; D019884:Nitrogenous Group Transferases; D019759:Carbon-Nitrogen Lyases; C505161:At2g38230 protein, Arabidopsis; D008239:Lysine