SUPPLEMETARY IFRMATI doi:1.138/nature1152 6 1 6 Absorbance at 28 nm (mau) 5 4 3 2 1 15 kda 1 kda 75 kda 5 kda 37 kda 25 kda 2 kda 15 kda marker wt H153 1 5 1 4 Molar mass (Da) 5 1 15 2 Elu on volume (ml) 1 3 Supplementary Figure 1. ligomeric state and purity of. Recombinant is dimeric as determined by gel filtration chromatography (blue, left axis) and multi-angle light scattering (red, right axis) and is highly purified as assessed by SDS-PAGE (inset). WWW.ATURE.CM/ATURE 1
RESEARCH SUPPLEMETARY IFRMATI Ipsaro, Haase et al. H153 scpld Extract phospholipase buffer blank wt H153 scpld Extract nuclease buffer blank wt H153 scpld blank wt Defined phospholipase buffer H153 scpld Defined nuclease buffer blank wt a CL PE PS PC PA origin b 2 2 15 1 1 5 5 c no protein wildtype H153 scpld6 16 Intensity in thousands (CL) 14 16 Cardiolipin Phospha dic acid 14 12 12 1 1 8 8 6 6 4 4 2 2 Intensity in thousands (PA) 15 no protein wildtype H153 scpld6 Intensity in thousands (PA) Intensity in thousands (CL) Cardiolipin Phospha dic acid Supplementary Figure 2. Phospholipase activity was not detected for. a) A TLC-based assay was used to evaluate cardiolipin cleavage. Defined liposomes (PC:PE:PS:CL at 2:2:1:1) or extract-based liposomes (made with bovine heart lipid 2 W W W. A T U R E. C M / A T U R E
SUPPLEMETARY IFRMATI RESEARCH extract supplemented with CL) were incubated with purified under various conditions. In every case, wild-type and catalytically inactive H153 showed no detectable cleavage of cardiolipin or formation of PA. In contrast, a known phospholipase D from S. chromofuscus completely eliminated CL from each reaction. Lipid identification was based on standards run in parallel. Migration distances for the standards are indicated to the right of the TLC plates. b-c) SRM-MS was used to monitor the disappearance of CL and appearance of PA for defined liposome reactions under (b) phospholipase and (c) nuclease buffer conditions. o significant changes were observed for reactions containing /PLD6. The positive control showed complete hydrolysis of CL and a striking increase in the abundance of PA. Error bars indicate ± the standard deviation. ote that panel b is duplicated from the main text but is reproduced here for the convenience of the reader. WWW.ATURE.CM/ATURE 3
RESEARCH SUPPLEMETARY IFRMATI a wt EDTA Mg 2+ Mn 2+ Ca 2+ Cu 2+ Zn 2+ 2 3.1 [mm] 5-4 - 3 - b wt H153 scpld a 3 V 4 + + + 7-6 - 5-4 - 3 - c datp ddatp TdT 7-6 - 5 - wt + + + + H153 + + + + 2-4 - 2-3 - 1-1 - 2 - Supplementary Figure 3. shows single-strand (ss) endonuclease activity in vitro. a) catalysis does not require divalent cations as evidenced by ssdase activity in the presence of EDTA. While divalents were not required, certain ions (Ca 2+, Mn 2+, and Zn 2+ ) enhanced the activity. b) cleaves ssra in vitro. As is the case for the ssdase activity, addition of 4 mm a 3 V 4 or the H153 mutation abolishes the ssrase activity of. Phospholipase D from Streptomyces chromofuscus (scpld) did not exhibit nuclease activity. Reactions were analyzed by Urea-PAGE (15%). c) releases DA products with 3 H termini. DA fragments are extracted from cleavage reaction and incubated with Terminal deoxynucleotidyl Transferase (TdT) in the presence of ddatp or datp (as indicated). 4 WWW.ATURE.CM/ATURE
SUPPLEMETARY IFRMATI RESEARCH a Gl u B 181 His A 153 His B 153 Gl u A 181 H H H R'H R P R' Gl u B 181 His A 153 H P H H R His B 153 H Gl u A 181 R P H Gl u B 181 His A 153 His B 153 Gl u A 181 H H H b 12 12 1 Intensity 1 8 6 4 Transi ons from unmodified pep de GYMHHK y6 ion 772.36 + YMHHK y5 ion 715.33 + LGYMHHK y7 ion 885.44 + DLGYMHHK y8 ion 1.47 + Intensity 8 6 4 2 5 1 15 2 25 3 Reten on me (min) Transi ons from phosphopep de AGIQVR b6 ion 625.38 + p(mhhk) y4 ion 632.27 + AGIQVRH b7 ion 762.44 + 2 16.5 17. 17.5 18. 18.5 19. 19.5 Reten on me (min) Supplementary Figure 4. proceeds through a phosphohistidine intermediate and binds nucleic acids directly. a) As proposed by Dixon and colleagues 15,18, the HKD phosphodiesterase mechanism consists of two distinct steps. In the first step, the lone pair of the imidazole nitrogen of His A 153 attacks the scissile phosphate leading to an S 2 reaction and the formation of a covalent phosphohistidine intermediate. The leaving group then abstracts a proton from the opposing (protonated) His B 153. In the second step, a proton is abstracted from water by the deprotonated His B 153. The activated water then attacks the phosphohistidine intermediate resulting in product release. b) SRM-MS was used to confirm and further pinpoint the location of the phosphistidine intermediate. Chromatograms show the transition ion intensity for numerous fragments from the phosphorylated (red, orange, yellow traces) and unphosphorylated (green, blues, purple traces), +4 charge state, His 153-containing peptide precursors. Based on the ions observed, the location of the phosphorylation could be mapped to residues 152-154. WWW.ATURE.CM/ATURE 5
RESEARCH SUPPLEMETARY IFRMATI ormalized anisotropy difference 1 8 6 4 2 (wt) with DA (wt) with RA (H153) with DA (H153) with RA Calculated K D values (wt) with DA (wt) with RA (H153) with DA (H143) with DA 38.7 ± 1.4 nm 55.7 ± 12.5 nm 51.2 ± 12.9 nm 7.5 ± 16.1 nm.5 1. 1.5 2. 2.5 Protein concentra on (μm) Supplementary Figure 5. binds ssda and ssra with comparable affinity. Binding affinity measurements for (wildtype and H153 mutant) with both ssda and ssra were measured using fluorescence polarization. The affinity in each case is roughly 5 nm. 6 WWW.ATURE.CM/ATURE
SUPPLEMETARY IFRMATI RESEARCH Ser A 168 Gl u A 181 H H 2.61 Asn A 17 H 2.82 H 2 2.67 3.38 2.61 2.93 Lys A 155 H His B 153 2.55 2.67 H 3 2.92 2.94 H W H 2.94 2.92 H 3 2.67 2.55 His A 153 H Lys B 155 2.93 2.61 2.67 H 2 2.82 H Asn B 17 3.38 2.61 H H Gl u B 181 Ser B 168 Supplementary Figure 6. The hydrogen bond network of. Similar to that observed in the structure of uc 18, has an extensive active site hydrogen bonding network which spans the dimerization interface. Side chains for monomer A are in red, side chains for monomer B are in blue, tungstate is in purple, and hydrogen bonds are indicated as dashed grey lines. Distances are expressed in Å and indicate the separation of the non-hydrogen nuclei. The distance from ε of His153 to the tungsten atom is 3. Å. WWW.ATURE.CM/ATURE 7
H H RESEARCH SUPPLEMETARY IFRMATI a Zn 2+ α5 β4 α4 Zn 2+ β2 β3 α3 β1 β8 α6 β7 β5 α2 cytoplasm α1 outer mitochondrial membrane intermembrane space b Cys A 49 Zn 2+ Cys A 68 c Anomalous Map Contour Levels 1σ 15σ His A 72 Cys A 66 d Asn B 17 His A 153 e Anomalous Map Contour Levels 5σ 1σ Lys B 155 W 4 2- Lys A 155 His B 153 Asn A 17 Supplementary Figure 7. Coordination geometries of bound ligands. a) Stylized drawing of the structure. The active site is formed by the dimerization interface with the zinc wings extending away from the center of the homodimer. b) An unexpected CCCH zinc wing was found in the protein consisting of residues Cys49, Cys66, Cys68, and His72. c) The identity of the Zn 2+ was confirmed by calculating anomalous difference maps for datasets collected from the same crystal above (contoured at 1 and 15σ) and below the Zn 2+ K edge (no signal detectable above the noise). d) co-crystallized with tungstate bound tungstate exclusively in the active site. e) The anomalous difference map (contoured at 5 and 1σ) indicates the presence an anomalous scatterer in the active site only for the tunstate-containing co-crystals. 8 WWW.ATURE.CM/ATURE
b a (dsda) uc 1BYR (dsda) BfiI 2C1L (phospholipids) 2ZE9 PLD 3HSI PC Synthase (phospholipids) (phospha dyl choline) 1FI PLD Supplementary Figure 8. Comparative analysis of PLD family members with HKD motifs. a) Electrostatic surfaces of an array of PLD family members in the same orientation illustrate the utilization of specific structural contexts to convey substrate specificity. In the case of the nucleic acid phosphodiesterases (PDB IDs: 1BYR18, 2C1L31, and this structure), a long, positively-charged groove runs through the active site. For the phospholipases (PDB IDs: 2ZE9, 1FI32, 3HSI), a deep pocket accommodates the substrate. Each surface depicts the solvent-accessible surface contoured at ± 2 kbt/e. Surfaces were calculated using APBS3 with a solvent ion concentration of.15 M. b) Ribbon diagrams of each molecule in the same orientation as in (a). ote that the overall fold and position of the active site remains consistent in each case, with additional structural elements decorating the core. (ssda, ssra) SUPPLEMETARY IFRMATI RESEARCH Ipsaro, Haase et al. W W W. A T U R E. C M / A T U R E 9
RESEARCH SUPPLEMETARY IFRMATI Ipsaro, Haase et al. 9 Q top-down view ac ve site (cytoplasmic surface) side view 9 Q (membrane surface) underside view Supplementary Figure 9. Various views of the electrostatic surface. In addition to the positively-charged groove which spans the active site, two negative patches are present on the top surface of the dimer. Another positively charged patch is also present on the underside of the protein, which may serve to strengthen the attachment of the protein to the negatively-charged phospholipid head groups on the surfaces of the underlying mitochondrial membrane. Each surface depicts the solventaccessible surface contoured at ± 2 kbt/e. Surfaces were calculated using APBS3 with a solvent ion concentration of.15 M. The active site region is indicated with a dashed circle in the top-down and side views. 1 W W W. A T U R E. C M / A T U R E
SUPPLEMETARY IFRMATI RESEARCH Ipsaro, Haase et al. a top-down view side view b scissile phosphate AsnA17 HisA153 LysB155 HisB153 LysA155 AsnB17 Supplementary Figure 1. Views of RA in the active site groove. a) Using the structure of the, a short RA molecule was manually built into the model then subjected to energy minimization using GRMACS25. The minimized model (RA in green) shows the phosphates of the RA backbone positioned in the most positively charged areas of the groove with the bases extending away from the dimer core. b) A close-up view of the active site places the RA (purple) in the active site groove with the scissile phosphate (circled) situated directly between the catalytic histidines. Conserved active site residues are shown as sticks (grey) overlaid on the ribbon diagram (colored as in Fig. 3, faded). W W W. A T U R E. C M / A T U R E 1 1
RESEARCH SUPPLEMETARY IFRMATI Supplementary Table 1. Data collection and refinement statistics + a 2W 4 Data collection Space group P4 32 12 P4 32 12 Cell dimensions a, b, c (Å) 38.7, 38.7, 214.5 38.9, 38.9, 213.3 α, β, γ ( ) 9, 9, 9 9, 9, 9 Above Zn 2+ peak Below Zn 2+ edge Wavelength 1.75 Å 1.2716 Å 1.2983 Å Resolution (Å) 4.-1.75 (1.85-1.75) 4.-2.1 (2.23-2.1) 4.-2.2 (2.32-2.2) R sym or R merge 4.8 (27.8) 5.9 (29.7) 5.7 (32.1) I/σI 21.3 (5.9) 24. (7.5) 24.8 (7.1) Completeness (%) 98.1 (98.8) 99.7 (98.5) 99.9 (1.) Multiplicity 6.8 (6.9) 1.2 (1.5) 1.2 (1.6) Refinement Resolution (Å) 4.-1.75 (1.8-1.75) 4.-2.1 (2.16-2.1) o. reflections 16154 / 862 (1143 / 65) 9676 / 514 (565 / 35) R work/ R free 17.5 / 19.7 (24.9 / 25.2) 2.9 / 25.1 (22.6 / 29.4) o. atoms Protein 1336 1316 Ligand/ion 1 (Zn 2+ ) 6 (1 Zn 2+ ; 1 W 2-4 ) Water 15 35 B-factors** Protein 28.3 41.6 Ligand/ion 33.4 (Zn 2+ ) 64.1 (Zn 2+ ) 49.3 (W 2-4 ) Water 23.1 24.5 R.m.s deviations Bond lengths (Å).11.13 Bond angles ( ) 1.281 1.382 *Highest resolution shell is shown in parenthesis. **The TLS contribution is included in the presented average B-factors. Supplementary Literature Cited 31 Grazulis, S. et al. Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DA-binding domain with a nonspecific nuclease. Proc atl Acad Sci U S A 12, 15797-1582, doi:1.173/pnas.5794912 (25). 32 Leiros, I., Secundo, F., Zambonelli, C., Servi, S. & Hough, E. The first crystal structure of a phospholipase D. Structure 8, 655-667 (2). 33 Bieniossek, C., Richmond, T. J. & Berger, I. MultiBac: multigene baculovirus-based eukaryotic protein complex production. Curr Protoc Protein Sci Chapter 5, Unit 5 2, doi:1.12/47114864.ps52s51 (28). 34 Pozharski, E. V., McWilliams, L. & MacDonald, R. C. Relationship between turbidity of lipid vesicle suspensions and particle size. Anal Biochem 291, 158-162, doi:1.16/abio.21.512 (21). 35 Vagin, V. V. et al. A distinct small RA pathway silences selfish genetic elements in the germline. Science 313, 32-324, doi:1.1126/science.1129333 (26). 36 Kabsch, W. Automatic Processing of Rotation Diffraction Data from Crystals of Initially Unknown Symmetry and Cell Constants. J Appl Crystallogr 26, 795-8 (1993). 37 Collaborative. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 5, 76-763, doi:1.117/s974449943112 (1994). 12 WWW.ATURE.CM/ATURE
SUPPLEMETARY IFRMATI RESEARCH 38 McCoy, A. J. et al. Phaser crystallographic software. J Appl Crystallogr 4, 658-674, doi:1.117/s21889872126 (27). 39 Perrakis, A., Harkiolaki, M., Wilson, K. S. & Lamzin, V. S. ARP/wARP and molecular replacement. Acta Crystallogr D Biol Crystallogr 57, 1445-145 (21). 4 Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 6, 2126-2132, doi:1.117/s974449419158 (24). 41 Murshudov, G.., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53, 24-255, doi:1.117/s9744499612255 (1997). 42 Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66, 12-21, doi:1.117/s97444994273 (21). 43 DeLano, W. L. The PyML Molecular Graphics System. (22). 44 Holm, L. & Rosenstrom, P. Dali server: conservation mapping in 3D. ucleic Acids Res 38, W545-549, doi:1.193/nar/gkq366 (21). 45 Lindorff-Larsen, K. et al. Improved side-chain torsion potentials for the Amber ff99sb protein force field. Proteins 78, 195-1958, doi:1.12/prot.22711 (21). 46 Essmann, U. et al. A Smooth Particle Mesh Ewald Method. J Chem Phys 13, 8577-8593 (1995). WWW.ATURE.CM/ATURE 13