5lnr | pdb_00005lnr

Crystal structure of Arabidopsis thaliana Pdx1-PLP complex

spinqualitylabelsall models 5lnr, resolution 1.61Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5lnr is a 4 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: GOL, PLP Gene: PDX13, GIP2, PDX1L3, RSR4, At5g01410, T10O8.120 (ARATH) Activity: Pyridoxal 5'-phosphate synthase (glutamine hydrolyzing), with EC number 4.3.3.6 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [PDX13_ARATH] Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by PDX2. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively. Also plays an indirect role in resistance to singlet oxygen-generating photosensitizers. Publication Abstract from PubMed 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 I320 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 beta6 of the Pdx1 (betaalpha)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 A between substrate- and product-binding sites. Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis.,Rodrigues MJ, Windeisen V, Zhang Y, Guedez G, Weber S, Strohmeier M, Hanes JW, Royant A, Evans G, Sinning I, Ealick SE, Begley TP, Tews I Nat Chem Biol. 2017 Jan 16. doi: 10.1038/nchembio.2273. PMID:28092359 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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