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1 SUPPLEMENTARY FIGURES
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3 Supplementary Figure 1 Protein sequence alignment of Vibrionaceae with either a 40-residue insertion or a 44-residue insertion. Identical residues are indicated by red background. Incomplete identities among aligned sequences are in red text. The alignment was prepared with ClustalW 1 and ESPript (
4 Supplementary Figure 2 Temperature factor distribution in the three FadR structures is shown as B- factor putty as implemented by PyMOL ( The C-atom B-factors are depicted on the structure in dark blue (lowest B-factor) through to red (highest B-factor), with the radius of the ribbon increasing from low to high B-factor. Only one monomer is shown for each structure for clarity. Residue G66 at the tip of the wing of the winged-helix motif, is indicated by a * for orientation. Arrows indicate the positions of residues F74 and I97, which contains the short helical linker α4 (residues 81-89) in the apo and DNA-bound structures; this region becomes much more flexible (including α4 melting ) in the ligand-bound structure. (a) apo-fadr: the highest B factor region includes residues 64 to 74 (the wing of the HTH region). (b) FadR-DNA complex: the insertion region has the highest B factors. (c) FadR-ligand complex: the entire N-terminal DNA binding domains has comparatively high B-factors, and the region including helix α4 has melted and has the highest B-factors. All four oleoyl-coa ligands are shown as grey spheres.
5 Supplementary Figure 3 Schematic overview of the FadR-DNA contacts calculated by NUCPLOT 3. (a) V. cholerae. (b) E. coli (PDB 1H9T) 4. Bases are represented by one-letter codes. Bases making standard H-bonding base-pair interactions are connected by a solid black line. The DNA backbone is drawn next to the bases: the sugars as brown pentagons and phosphates as purple circles. The base numbers, as given in the PDB file, are inside the sugars. Interactions are plotted on either side of the
6 strands; interacting protein residues are represented by their atom name, residue name, number and the chain identifier (A or B) in parentheses with hydrogen bonds as blue dotted lines and non-bonded contacts (<3.35Å) as red dotted lines. Atom names are blue for nitrogen and red for oxygen; here, atom names are omitted from residues interacting only by non-bonded contacts. Water molecules are drawn as blue circles and labeled by their PDB number 3. The DNA chains are labeled C, D for V. cholerae and X, Y for E. coli.
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8 Supplementary Figure 4 Electron density showing oleoyl-coa binding to FadR. (a) Fo-Fc electron density at 3.0σ for ligand site #1 of chain A. (b) Fo-Fc density at 2.3σ for ligand site #2 of chain B. Note the tail region of the site #2 ligand is in contact with the tail region of the adjacent monomer, and as such appears to be flexible and less well defined than regions of the ligand that form close contacts with the protein, as well as the tail region of the site #1 ligand shown in (a). In both panels, the ligand and alpha carbon trace of the final refined structure as described in the manuscript is shown for reference, with carbons in green. The alpha carbon trace following simulated annealing refinement with the ligand at the specific site omitted is shown in yellow and yellow sticks for the non-omitted ligand molecules. Positive electron density is shown in blue, and negative density is shown in green. (c) Stereo view of 2Fo-Fc electron density at 1.0σ for ligand site #1 of chain A. All panels in this figure were made using the auto open mtz option of Coot 5, followed by export using the Screenshot Raster3D option; final rendering was done using PyMOL (
9 Supplementary Figure 5 Two-dimensional diagrams showing interactions between VcFadR and oleoyl- CoA as calculated by LIGPLOT 6. (a) The ligand binding pocket similar to that of E. coli (site #1, monomer A). The ligands and protein side chains are shown in ball-and-stick representation, with the ligand bonds in purple and protein bonds in orange. Hydrogen bonds are green dashed lines with indicated distances (in Å). Residues in hydrophobic contact with the ligand are represented by red semicircles with radiating spokes. The atoms are colored as follows: nitrogen, blue; oxygen, red; carbon, black; sulfur, yellow; phosphorous, purple. (b) The ligand binding pocket involving the insertion region (site #2, monomer A). Colors are the same as in (a).
10 Supplementary Figure 6 The interaction of oleoyl-coa (site #1, monomer B) with VcFadR. The conformation of the phosphorylated adenosine head group of oleoyl-coa bound to site #1 in monomer B is different from that bound to site #1 in monomer A. (a) The structure of oleoyl-coa bound to site #1 in monomer B, highlighting critical residues interacting with the ligand. Positively charged residues that interact with ligand phosphates are in blue. Residues forming hydrogen bonds are cyan, and those forming hydrophobic interactions are in green. (b). Two-dimensional diagram showing interactions between VcFadR and oleoyl-coa (site #1, monomer B) as calculated by LIGPLOT 6. Colors are the same as in Supplementary Fig. 5.
11 Supplementary Figure 7 Stereo view showing the superposition of VcFadR-oleoyl-CoA complex and EcFadR-myristoyl-CoA complex (PDB 1H9G). Carbon atoms are colored salmon in VcFadR and slate blue in EcFadR. VcL208 and EcM168 are labeled. Carbon atoms are colored magenta in oleoyl-coa and cyan in myristoyl-coa. The black arrow indicates double bond between C9 and C10 in oleoyl-coa. Other atoms are colored as follows: nitrogen, blue; oxygen, red; sulfur, yellow.
12 Supplementary Figure 8 Isothermal titration calorimetry (ITC) binding isotherm of VcFadR titrated with oleoyl-coa. Top, the raw heat signal from 29 injections of 10 μl aliquots of a 0.2 mm solution of oleoyl-coa into a cell containing mm VcFadR at 30 C; Bottom, the integrated area (heat) of each injection after background correction. ITC indicates that every monomer binds two molecules of oleoyl-coa (N 1 =1.1 and N 2 =0.8) with different thermodynamic parameters. K a = ± M -1 and M -1, H = ± 1.75 kcal/mol and ± 0.21 kcal/mol, G = kcal/mol
13 and kcal/mol, -T S = kcal/mol and kcal/mol for binding site #1 and site #2 of oleoyl- CoA, respectively. The reported values were derived from duplicate measurements. The difference in the free energy change between the two binding steps, G 1 G 2, is -1.7 kcal/mol, resulting in the second oleoyl-coa molecule binding VcFadR with a roughly 10-fold lower affinity than the first oleoyl- CoA. Binding of the second oleoyl-coa is accompanied by a more favorable enthalpy change ( H 2 - H 1 = -9.9 kcal/mol). By contrast, the second oleoyl-coa binds VcFadR with a much less favorable entropy change than the first oleoyl-coa, amounting to an entropic penalty [(-T S 2 ) - (-T S 1 ) = 11.6 kcal/mol]. Thus, the thermodynamic basis for the observed roughly 10-fold difference in the affinity of oleoyl-coa for these two sites is entirely entropic in nature. The pink and yellow spheres denote sites #1 and #2, respectively.
14 Supplementary Figure 9 The helix to loop transition in linker helix 4 upon ligand binding. (a) V. cholerae apo-fadr structure shown in two orientations. 4 in helix conformation is red, the rest of the protein is white. (b) VcFadR-ligand structure shown in two orientations. 4 in loop conformation is red, the rest of the protein is white. (c) The region boxed in (a) showing extensive and conserved hydrophobic interactions of 4 with the two flanking domains, the N-terminal DNA binding domain (residues involved in interactions shown in cyan) and the C-terminal ligand binding domain (residues involved in interactions shown in yellow).
15 Supplementary Figure 10 Comparison of effector mediated conformational changes between VcFadR and EcFadR. (a) Superposition of the structures of VcFadR-DNA complex and VcFadR-ligand complex. The DNA binding domain is in magenta (VcFadR-DNA complex) or cyan (VcFadR-ligand complex) and the rest of the protein is white. The distance between the two DNA recognition helices (R45 at the beginning of helix ) is 65 Å in VcFadR-ligand structure whereas that in the VcFadR-DNA complex is 15 Å. (b) Superposition of the structures of EcFadR-DNA complex (PDB 1H9T) 4 and EcFadR-ligand complex (PDB 1H9G) 4. The DNA binding domain is magenta (EcFadR-DNA complex) or green (EcFadR-ligand complex) and the rest of the protein is white. The distance between the two DNA recognition helices (R45, at the beginning of helix ) is 23 Å in EcFadR-ligand structure whereas that in the EcFadR-DNA complex is 15 Å.
16 Supplementary Table 1. Oligonucleotides used in this study Designation WS1 WS2 FabA1 FabA3 Chr1 Chr2 LacNot LacBgl FadE1 FadE3 FadH1 FadH3 FadB1 FadB4 FabB3 FabB4 FadR1 FadR2 FadR3 FadR4 FadR5 FadR6 Sequence (5'-3') CTTAGGCAACTGGTCAAACCAGAACATAAAA TTTTATGTTCTGGTTTGACCAGTTGCCTAAG GATCGGCGGCCGCAACGTTTGTTCTGCATTATTGG GATCGAGATCTAGTGCCTTGAATCTTGATGG GATCGGCGGCCGCGATATCATGCTAACGATTTTTAGAAC GATCGGAATTCGACCGCCACCAAACACTAAG GATCGGCGGCCGCGATCCGGGCATTGAGCAGTC GATCGAGATCTTCGCAACCAGATGATTGAGG GATCGGCGGCCGCAGAGAGCAAGATTTCCATAC GATCGGAATTCGCATCACAATGCGAACCACC GATCGGCGGCCGCGAGAGGCTGAAATAGATTTGGG GATCGGAATTCGAGCTCTTCACCAAACACG GATCGGCGGCCGCGTAAATCATTGTCTATCTCC GATCGGAATTCATGAGACCCCGTGAGCTGAG GATCGGCGGCCGCGACTCGTTTCATGTAACATTC GTTCCTGCGTCGTTCCAGC GATCGAGATCTTGCGTAACGAGTTGGATGTG GATCGGCGGCCGCAGACGATTGCTAATCTAGCACTG GATCGGCGGCCGCTGCCTTAATGACCATTAATG GATCGGAATTCCAGCTAAGTCACTCCCTGAG GGGAATCGCATATGGTCATTAAGGCAAAAAGCC GATCGGCTCTTCAGCACGCGCAATCGTCTTCAGTAAAATTG
17 Supplementary Methods ITC experiments Calorimetric titrations of VcFadR with oleoyl-coa were performed on a VP-Isothermal titration calorimeter (MicroCal). To improve baseline stability, the temperature of the system was kept about 5 C below the working temperature. Protein samples were buffer exchange to ITC buffer containing 20 mm Tris-HCl (ph 7.0), 50 mm NaCl, 1mM EDTA, 0.1 mm Tris (2 carboxyethyl) phosphine hydrochloride. The ligand solution was prepared by dissolving oleoyl-coa (Sigma) in the flow-through of the last buffer exchange. When establishing protein concentration, the monomeric molecular weight g/mole was used. The VcFadR protein concentration was measured spectrophotometrically at 280 nm using calculated molar extinction coefficient (M -1 cm -1 ) of Each titration typically consisted of two preliminary 2-µl injections followed by 29 subsequent 10-µl injections. Each injection consisted of 10 µl of a 0.2 mm solution of oleoyl-coa into a cell containing mm VcFadR at 30 C with a 10 sec duration and a 300 sec interval between injections. The syringe was rotated at 300 rpm during the experiment to assure immediate mixing. Data for two preliminary 2 µl injections were discarded. The heat of dilution control (titration of ligand into buffer) was subtracted from the titration. Raw data were integrated, corrected for nonspecific heat, and fit using the two sets of binding sites model embedded in Origin 7.0 (Microcal). The ITC experiments were highly reproducible, and the reported values were derived from duplicate measurements. Calculations of interactions Hydrogen bonds and van der Waals contacts in FadR-DNA complex structure were calculated using the program HBPLUS and plotted by NUCPLOT 3. To identify hydrogen bonds, the program finds all proximal donor (D) and acceptor (A) atom pairs that satisfy specified geometrical criteria for bond formation. Theoretical hydrogen atom (H) positions are then calculated for those donor atoms that fit the criteria and bonds are calculated between the hydrogen and acceptor atoms. The criteria used for the current study are: the H-A distance is <2.7 Å, the D-A distance is <3.0 Å, the D-H-A angle is >90 and the H-A-AA angle is >90, where AA is the atom attached to the acceptor. All atoms not involved in hydrogen bonds but separated by <3.35 Å were considered to be interacting through van der Waals contacts. NUCPLOT uses the list of interactions generated by HBPLUS to plot all H-bonds and nonbonded interactions between the protein and nucleic acid, between water and nucleic acid, and between
18 protein and nucleic acid via a bridging water molecule. Hydrogen bonds and non-bonded interactions in FadR-ligand complex structure were calculated using the program HBPLUS and plotted by LIGPLOT 6. To identify hydrogen bonds, the program computes all possible positions for hydrogen atoms (H) attached to donor atoms (D) which satisfy specified geometrical criteria with acceptor atoms (A) in the vicinity. The criteria used for the current study are: the H-A distance is <2.7 A, the D-A distance is <3.3 A, the D-H-A angle is >90 and the H- AAA angle is >90, where the AA atom is the one attached to the acceptor, usually preceding it along the amino acid chain. LIGPLOT uses the list of interactions generated by HBPLUS to plot all H-bonds between protein and ligand. All atoms not involved in hydrogen bonds but separated by <3.9 Å were considered to be interacting through non-bonded contacts. LIGPLOT uses the list of interactions generated by HBPLUS to extract and plot all hydrophobic interactions between pairs of carbon atoms between protein and ligand. Supplementary References 1. Larkin, M. A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, (2007). 2. Gouet, P., Robert, X. & Courcelle, E. ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res. 31, (2003). 3. Luscombe, N. M., Laskowski, R. A. & Thornton, J. M. NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions. Nucleic Acids Res. 25, (1997). 4. van Aalten, D. M., DiRusso, C. C. & Knudsen, J. The structural basis of acyl coenzyme A- dependent regulation of the transcription factor FadR. EMBO J. 20, (2001). 5. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, (2004). 6. Wallace, A. C., Laskowski, R. A. & Thornton, J. M. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein. Eng. 8, (1995).
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