5LNW

Crystal structure of Arabidopsis thaliana Pdx1-I320-G3P complex

Summary for 5LNW

• Entry DOI: 10.2210/pdb5lnw/pdb
• Descriptor: Pyridoxal 5'-phosphate synthase subunit PDX1.3, [(2~{R},3~{R})-2,3-bis(oxidanyl)-3-[[(2~{S})-3-oxidanylidenepent-4-en-2-yl]amino]propyl] dihydrogen phosphate, 5-O-phosphono-beta-D-ribofuranose, ... (6 entities in total)
• Functional Keywords: beta/alpha barrel, pyridoxal phosphate synthase, glutamine amidotransferase, vitamin b6 biosythesis, lyase
• Biological source: Arabidopsis thaliana (Mouse-ear cress)
• Total number of polymer chains: 4
• Total formula weight: 139794.86

Authors

Rodrigues, M.J.,Windeisen, V.,Zhang, Y.,Guedez, G.,Weber, S.,Strohmeier, M.,Hanes, J.W.,Royant, A.,Evans, G.,Sinning, I.,Ealick, S.E.,Begley, T.P.,Tews, I. (deposition date: 2016-08-06, release date: 2017-01-18, Last modification date: 2020-07-29)

Primary citation

Rodrigues, M.J.,Windeisen, V.,Zhang, Y.,Guedez, G.,Weber, S.,Strohmeier, M.,Hanes, J.W.,Royant, A.,Evans, G.,Sinning, I.,Ealick, S.E.,Begley, T.P.,Tews, I.
Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis.
Nat. Chem. Biol., 13:290-294, 2017

PubMed 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 I 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 β6 of the Pdx1 (βα)-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.

PubMed: 28092359
DOI: 10.1038/nchembio.2273

Experimental method

X-RAY DIFFRACTION (1.9 Å)