Supplementary Information to Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis Matthew J. Rodrigues 1,2, Volker Windeisen 1,3, Yang Zhang 4, Gabriela Guédez 3, Stefan Weber 3, Marco Strohmeier 3, Jeremiah W. Hanes 4,5, Antoine Royant 6,7, Gwyndaf Evans 2, Irmgard Sinning 3, Steven E. Ealick 4, Tadhg P. Begley 8, Ivo Tews 1,3,* 1 Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK 2 Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK 3 Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany 4 Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA 5 Pacific Biosciences, 1380 Willow Rd., Menlo Park, CA 94025, USA 6 Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, 38044 Grenoble, France 7 European Synchrotron Radiation Facility, 38043 Grenoble, France 8 Department of Chemistry, Texas A&M University, College Station, TX 77843, USA *Corresponding author 1
Supplementary Results Supplementary Table 1 Crystallographic Analysis R5P K166R I 320 I 320 I 320-G3P PLP prei 320 single multi crystal crystal 1 Data collection Space group R3 R3 R3 R3 R3 R3 Cell Dimensions a, b, c (Å) 176.73, 177.90, 178.12, 178.58, 178.26, 178.56, 176.73, 177.90, 178.12, 178.58, 178.26, 178.56, 114.65 115.02 115.96 117.38 115.31 116.88 α, β, γ ( ) 90,90,120 90,90,120 90,90,120 90,90,120 90,90,120 90,90,120 Resolution (Å) 24.79-1.91 24.74-2.32 52.20-1.73 46.75-2.24 44.57-1.90 40.26-1.61 (1.94-1.91) (2.35-2.32) (1.76-1.73) (2.29-2.24) (1.93-1.90) (1.64-1.61) R merge 0.056 0.095 0.054 0.216 0.123 0.049 (0.308) (0.336) (0.445) (1.361) (0.861) (0.475) CC(1/2) 0.996 0.997 0.978 0.977 0.998 (0.812) (0.841) (0.426) (0.447) (0.799) I / σi 11.4 (2.0) 9.5 (2.8) 9.3 (1.9) 30.5 (2.7) 6.1 (1.3) 9.0 (1.5) Completeness (%) 99.9 (100.0) 99.9 (100.0) 98.1 (99.7) 99.3 (99.2) 99.4 (97.8) 100.0 (100.0) Redundancy 3.8 (3.7) 5.7 (5.6) 2.9 (2.9) 4.3 (4.2) 3.2 (3.0) 2.8 (2.8) Wilson B 21.3 33.7 18.6 26.4 26.6 19.3 Refinement 5LNS 5LNT 5LNU 5LNV 5LNW 5LNR Resolution (Å) 24.79-1.91 24.74-2.32 46.35-1.73 46.75-2.24 44.57-1.90 40.26-1.61 No. Reflections 103359 58635 141161 65127 107047 179959 R work / R free 0.158/0.189 0.147/0.196 0.162/0.191 0.177/0.220 0.181/0.220 0.123/0.165 No. Atoms Protein 8405 7959 8357 8300 8166 8834 Ligand/ion 124 104 68 68 180 144 Water 859 412 1037 573 516 1070 B-factors Protein 29.4 36.3 22.9 29.9 34.4 28.4 Ligand/ion 23.8 41.6 30.3 36.8 42.9 27.8 Water 32.5 36.4 33.8 31.4 35.3 43.5 R.m.s. deviations Bond lengths (Å) 0.006 0.007 0.006 0.011 0.006 0.005 Bond angles ( ) 0.800 0.838 0.813 1.355 0.934 0.709 Data were collected from one crystal for each structure. 1 Data merged from 19-wedges coming from 9 crystals, see Online Methods. *Values in parentheses are for highest-resolution shell. 2
Supplementary Figure 1 Simulated annealing omit maps for the crystallographic complexes reported in this study. a, Pdx1- R5P. b, K166R-preI 320. c, Pdx1-I 320. d, Pdx1-I 320 -G3P. e, Pdx1-PLP. In each case, the intermediate ligand atoms were omitted from the map calculation using simulated annealing refinement in CNS (SA-omit-map protocol with default parameters) 54. The F o -F c electron density map is shown as green mesh at 10σ for Pdx1-R5P, K166R-preI 320, Pdx1-I 320 and Pdx1-PLP and at 5σ for Pdx1-I 320 - G3P. The model shown is that of the refined complexes, as reported in the main paper. Carbon atoms are red, oxygen atoms purple, phosphorous atoms grey, nitrogen atoms blue. Figure prepared with Coot 55. 3
Supplementary Figure 2 Interactions between Pdx1 and intermediates of PLP synthesis. The figure shows interactions for the crystallographic complexes reported in this study: a, Pdx1-R5P. b, K166R-preI 320. c, Pdx1-I 320. d, Pdx1-I 320 -G3P. e, Pdx1-PLP. In each case, the carbon atoms are black with bonds shown for protein amino acids in black and for intermediates in purple, oxygen atoms red, phosphorous atoms purple, nitrogen atoms blue. Hydrophobic interactions are shown as van-der-waals spheres. Figure prepared with Ligplot 56. 4
Supplementary Figure 3 Low dose Pdx1-I 320 multi-crystal experiment. The diffraction data were collected from nine crystals at limiting dose of 245 kgy and merged in BLEND to 2.2 Å resolution 31. a, 2F o -F c map after refinement contoured at 1σ. Lysine N-ε is cyan, I 320 carbon atoms orange, nitrogen atoms blue, and oxygen atoms red. b, Simulated annealing F o -F c electron density map shown as green mesh at 10σ for Pdx1- I 320 ; carbon atoms are red, oxygen atoms purple, phosphorous atoms grey, nitrogen atoms blue; see legend of Supplementary Fig. 1 for details. 5
Supplementary Figure 4 Structural changes of Pdx1 support I 320 intermediate formation. a, Selected structure elements of Pdx1 are shown in cartoon representation. The side chain of the catalytic Lys166 has a different orientation in the Pdx1-R5P and in the Pdx1-I 320 complexes and is shown as red and purple sticks, respectively, nitrogen atoms blue. Coloured dots indicate the Cα-positions for Thr165 and Gly167.b. UV-Vis spectrum of a Pdx1-I 320 and a Pdx1-preI 320 crystal measured at ESRF beamlines ID14-1 and ID29 respectively 23,43. The spectrum of the Pdx1-I 320 crystal (yellow) shows an absorption maximum at 280 nm, corresponding to protein, and near 320 nm for the I 320 intermediate. The K166R variant (purple) shows reduced absorbance at 320 nm with the absorption maximum shifted to ~333 nm. c, The Ramachandran plot illustrates the changes in backbone conformation between the Pdx1-R5P and the K166R-preI 320 / Pdx1- I 320 complexes for amino acids Thr165, Lys166/Arg166 and Gly167. d, Cartoon representation of strand β6 and part of the β6-α6-loop on which the catalytic Lys166 is located. A peptide flip occurs at the Lys166-Gly167 peptide bond, supporting the different side chain orientation of Lys166 between the Pdx1-R5P (red) and the Pdx1-I 320 complexes (purple, left), and similarly between Arg166-Gly167 in the Pdx1-R5P (red) and the K166R-preI 320 complexes (green, right). e, Ammonia is produced by the Pdx1 associated glutaminase Pdx2 and allows conversion of the R5P adduct to I 320 (Pdx1-I 320 complex purple, Pdx1-R5P complex red). Ammonia is transferred from the Pdx2 active site through the central β-barrel of the Pdx1 enzyme, passing a constriction formed by amino acids Met162 and Met96. Mutagenesis data support a coupling of Pdx1 and Pdx2 6
enzymatic activities through these residues 15, suggesting that the conformational changes around Lys166 are coupled with ammonia transfer. Supplementary Figure 5 UV-Vis Spectra of Pdx1-PLP Crystals, UV-Vis spectra recorded at ESRF beamline ID14-1 from a Pdx1-PLP crystal 43. The spectrum of the crystal shows an absorption maximum at λ = 414 nm for covalently bound PLP (light green), while free PLP in the surrounding buffer has an absorption maximum of λ = 388 nm (dark green). The shift in absorbance maximum from 388 to 414 nm is characteristic for a covalent PLP complex 6,16. 7
Supplementary Figure 6 Mechanistic proposal for PLP biosynthesis by Pdx1, The mechanism begins with formation of an R5P imine 2, which tautomerizes to 3, and ends with a PLP imine 16. In this mechanism, Pdx1-preI 320 7 reacts with Lys166 to form Pdx1- I 320 9. This then reacts with G3P to form a further covalent intermediate 10. Release of Lys98 and transfer of this intermediate to the P2 site leads to the observed covalent PLP complex 16. Structures of intermediates 3, 7, 9, 10, and 16 were determined. 8
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