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1 Supporting Information Decoding Allosteric Networks in Biocatalysts: Rational Approach to Therapies and Biotechnologies Johannes T. Cramer 1,2, Jana I. Führing 1, Petra Baruch 2, Christian Brütting 3, Hans-Joachim Knölker 3 *, Rita Gerardy-Schahn 1 and Roman Fedorov 2 * 1 Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, Hannover, Germany 2 Institute for Biophysical Chemistry / Research Division for Structural Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, Hannover, Germany 3 Department of Chemistry, Technische Universität Dresden, Bergstrasse 66, Dresden, Germany Corresponding Authors * Fedorov.Roman@mh-hannover.de * hans-joachim.knoelker@tu-dresden.de S1
2 Table of Contents Supporting Tables... 3 Table S Table S Supporting Figures... 5 Figure S Figure S Figure S Figure S Figure S Figure S Figure S Figure S Figure S Figure S S2
3 Supporting Tables Table S1 LmUGP mutant crystal structure statistics LmUGP mutant V402W S374W S374F G45Y PDB-code 5NZH 5NZG 5NZI 5NZJ Crystal parameters Space group C 2 C C C Cell parameters: a, b, c[å], α, β, γ[ ] 179.6, 70.9, 112.3, 90, 123.5, , 89.8, 137.3, 90, 90, , 88.2, 137.4, 90, 90, , 87.7, 138.1, 90, 90, 90 Data collection Beamline Petra III P11 ESRF ID29 ESRF ID29 ESRF ID23-2 Wavelength [Å] Crystal mosaicity[ ] Wilson B-factor [Å 2 ] Resolution range (total/high)[å] / / / / Unique reflections (total/high) 26,339/2,510 78,616/13,410 30,193/3,929 35,684/4,915 Completeness (total/high) [%] 100.0/ / / /100 (I/σ(I)) (total/high) 4.37/ / / /2.25 Rsigma (total/high) % 18.3/ / / /45.5 Rint (total/high) % 26.3/ / / /76.3 Refinement statistics Included amino acids Protein atoms 7,465 3,731 3,731 3,731 H2O molecules Rwork/Rfree % 22.5/ / / /21.5 RMSD bonds [Å]/angles [ ] 0.007/ / / /1.314 S3
4 Table S2 LmUGP complex crystal structure statistics LmUGP complex Phenylalanine Resveratrol Murrayamine-I PDB-code 5NZK 5NZL 5NZM Crystal parameters Group C C P43 Cell parameters: a, b, c[å], α, β, γ[ ] 72.66, , , 90, 90, , , , 90, 90, , 95.11, 72.67, 90, 90, 90 Data collection ESRF beamline ID29 ID23-2 ID30B wavelength [Å] Crystal mosaicity [ ] Wilson B-factor [Å 2 ] resolution range (total/high)[ Å] / / / unique reflections (total/high) 22,170/2,219 24,020/2,733 27,167/3,182 completeness (total/high) % 100/ / /99.9 (I/σ(I)) (total/high) 17.27/ / /2.38 Rsigma (total/high) % 3.7/ / /40.1 Rint (total/high) % 9.8/ / /73.0 Refinement statistics included amino acids Protein atoms 3,731 3,731 3,731 H2O molecules Rwork/Rfree % 19.4/ / /22.4 RMSD bonds [Å]/angles [ ] 0.014/ / /0.663 S4
5 Supporting Figures Figure S1 LmUGP activities (A) LmUGP allosteric pocket mutant activities compared to the wild-type. (B) Effect of 600 µm resveratrol or phenylalanine on LmUGP activity. S5
6 Figure S2. Electron density omit map around murrayamine-i in allosteric pocket 1 of LmUGP shown in three orientations. S6
7 Figure S3 (A) Pharmacophore representation of pocket 1. Hydrophobic patches are shown in black, hydrogen bond donors and acceptors in blue and red, respectively. (B) Molecular scaffold for a model of pocket 1 inhibitor resulting from in silico and in crystal molecular fragment screening. (C) X-ray crystal structure of LmUGP phenylalanine complex. (D) X-ray crystal structure of LmUGP resveratrol complex. The color scheme used for the protein surface on panels (C) and (D) is the same as in Figure 1A of the main text. S7
8 Figure S4 (A) Superposition of LmUGP (green, red, magenta, grey) and hugp (black, blue) demonstrates highly conserved structures of the catalytic domains and active sites of the host and the pathogen s enzymes. At the same time, the lock region in LmUGP (grey) has significant differences from the corresponding area in hugp (blue). (B) Superposition of the lock region of LmUGP in the open (apo) and closed (post-reactive) states (grey and blue colors, respectively). The large-scale conformational change of the lock is essential for the stabilization of Glc-1P substrate and its optimal positioning for the catalytic reaction. S8
9 Figure S5 Kinetics for LmUGP V402W mutant. Depicted is the activity, dependent on UTP- or Glc-1P concentration and the resulting Km for both substrates. S9
10 Figure S6 X-ray crystal structure of LmUGP V402W mutant. (A) Overview and (B) close-up view of LmUGP in surface representation with the W402 surface in cyan. The color scheme used for the protein surface is the same as in Figure 1A of the main text. (C) Superposition of V402W mutant (black) and the wild-type (colored) structures. The semitransparent molecular surface shows the steric hindrance effect of tryptophan in pocket 1. (D) 2F o F c electron density omit map for W402 and (E) the active site lacking UDP-Glc. S10
11 Figure S7 X-ray crystal structure of LmUGP S374W mutant. (A) Overview and (B) close-up view of LmUGP in surface representation with the W374 surface in cyan. The color scheme used for the protein surface is the same as in Figure 1A of the main text. (C) 2F o F c electron density omit map for W374 and (D) UDP-Glc in the active site. S11
12 Figure S8 X-ray crystal structure of LmUGP S374F mutant. (A) Overview and (B) close-up view of LmUGP in surface representation with the F374 surface in cyan. The color scheme used for the protein surface is the same as in Figure 1A of the main text. (C) 2F o F c electron density omit map for F374 and (D) UDP-Glc in the active site. S12
13 Figure S9 X-ray crystal structure of LmUGP G45Y mutant. (A) Overview and (B) close-up view of LmUGP in surface representation with the G45 surface in cyan. The color scheme used for the protein surface is the same as in Figure 1A of the main text. (C) 2F o F c electron density omit map for G45 and (D) UDP-Glc in the active site. S13
14 Figure S10 The flow chart summarizing a rational approach to identify, analyze, validate and target specific allosteric regulation sites in biocatalysts with conserved catalytic centers. S14
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