Supporting Information

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1 Supporting Information Reaction Mechanism of Adenylyltransferase DrrA from Legionella pneumophila Elucidated by Time-Resolved Fourier Transform Infrared Spectroscopy Konstantin Gavriljuk, Jonas Schartner, Aymelt Itzen, Roger S. Goody, Klaus Gerwert, *, and Carsten Kötting *, Department of Biophysics, Ruhr-Universität Bochum, Universitätsstrasse 150, Bochum, Center for Integrated Protein Science Munich (CIPSM), Chemistry Department, Technische Universität München, Lichtenbergstrasse 4, Garching, Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund, Germany S1

2 Figure S1: Synthesis scheme of npe-caged PP i and γ- 18 O 3 -ATP. Organic synthesis of npeppi and npe-γ- 18 O 3 -ATP was done by the coupling of 1-(2-nitrophenyl)diazoethane with PPi or γ- 18 O 3 -ATP. 1-(2- nitrophenyl)diazoethane was prepared by a reaction with hydrazine, followed by the reduction using manganese dioxide. S2

3 Figure S2: (A) 31 P-NMR of npeppi triethylammonium salt. The peak at ppm can be assigned to the caged pyrophosphate. (B) 31 P-NMR of npe-γ- 18 O 3 -ATP triethylammonium salt. The α-phosphate can be assigned to ppm, the β-phosphate to ppm and the γ-phosphate to ppm according to Cherepanov, A. V.; Doroshenko, E. V.; Matysik, J.; de Vries, S.; De Groot, H. J. M. Phys Chem Chem Phys 2008, 10, S3

4 Figure S3: Structural alignment of DrrA, GS-AT, KNTase, and LinB. (A) Cartoon representation of aligned structures of DrrA (3L0I and 3NKU, cyan), GS-AT (3K7D, green), LinB (3JZ0, yellow), and KNTase (1KNY, red). The alignment was performed only for the loop containing the conserved catalytically important motif and the adjacent β-strands, shown in solid representation. The position of the nucleotide is that from the LinB structure. (B) Sequence alignment of the conserved catalytically important motif that is the basis of the structural alignment. Conserved acidic residues are highlighted in red. S4

5 Figure S4: Negative control and reaction kinetics with different GTPases. Time-dependent absorbance changes of the Tyr77-AMP band at 1089 cm -1 during adenylylation by DrrA in absence of PPase are shown. Data for Rab1b in the GDP-bound state (blue) are the same as in Figure 1. Adenylylation of Rab5a GDP (red), which is not a natural substrate of DrrA, still occurs under FTIR conditions (millimolar protein concentrations), but the reaction is 10-fold slower than with Rab1b. In the absence of a substrate GTPase, DrrA does not react with ATP (black). Monoexponential fits are shown as solid lines. The negative control has been fitted linearly, which shows the slight baseline drift present in this measurement. Figure S5: Photolysis spectra of npeatp in solution and in presence of DrrA. Amplitude spectra of the photolysis of free npeatp (blue) and npeatp in presence of DrrA and Rab1b (red) are compared. Negative bands belong to caged-atp, positive bands to ATP. Since the spectra are virtually the same, especially in the region of the asymmetric γ-phosphate (1143 cm -1 ) and the ATP combination (1123 cm -1 ) vibrations, it can be concluded that ATP is still in solution in its free form after photolysis in presence of DrrA and Rab1b. The formation of the DrrA ATP Rab1b complex is not resolved. Notably, no spectral changes of ATP were observed in presence of DrrA only, meaning that ATP binds to the complex of DrrA and Rab1b. S5

6 Figure S6: Assignment of the β-phosphate bands in the infrared spectra. Amplitude spectra of the adenylylation reaction steps using unlabeled (blue) and β- 18 O 3 -labeled (red) npeatp are compared. In the spectrum of k 1, negative bands belong to free Rab1b, DrrA, and ATP, positive bands to the complex of Rab1b-AMP with DrrA and pyrophosphate. In the spectrum of k 2, negative bands belong to the complex of Rab1b-AMP with DrrA and PP i, positive bands to free Rab1b-AMP, DrrA, and phosphate. The double difference (labeled - unlabeled) is shown in green. In the spectrum of k 1, the band shift at 1254 cm -1 indicates the disappearance of ATP. Since an α-atp vibration was also detected at 1258 cm -1 (Figure 3), the band belongs to a combination vibration of the α- and β-phosphates of ATP. The band shifting from 1143 cm -1 to 1086 cm -1 can be assigned to appearing pyrophosphate. Shifts of the ATP combination vibration band can be expected around 1122 cm -1, but these are not well visible, probably due to overlap with the pyrophosphate band shifts. In the spectrum of k 2, disappearing pyrophosphate is detected at 1146 cm -1, while appearing phosphate can be seen at 1080 and 990 cm -1. S6

7 Figure S7: Assignment of the γ-phosphate bands in the infrared spectra. Amplitude spectra of the adenylylation reaction steps using unlabeled (blue) and γ- 18 O 3 -labeled (red) npeatp are compared. In the spectrum of k 1, negative bands belong to free Rab1b, DrrA, and ATP, positive bands to the complex of Rab1b-AMP with DrrA and pyrophosphate. In the spectrum of k 2, negative bands belong to the complex of Rab1b-AMP with DrrA and PP i, positive bands to free Rab1b-AMP, DrrA, and phosphate. The double difference (labeled - unlabeled) is shown in green. In the spectrum of k 1, no clear shifts can be observed because the γ-phosphate and ATP combination bands (Figure S4) almost completely overlap with the pyrophosphate band (Figure S5). In the spectrum of k 2, however, the same pattern as with β- 18 O 3 -labeling is observed: disappearing pyrophosphate is detected at 1148 cm -1, while appearing phosphate can be seen at 1078 and 990 cm -1. Figure S8: Comparison of the ATP interaction pattern in LinB, and DrrA. (A) ATP-binding pocket of LinB, PDB 3JZ0 (Ref. 35). (B) A cartoon depicting the arrangement of ATP-binding or catalytic residues in DrrA. Two positively charged residues and two hydroxyl sidechains are present in each case, while DrrA has four relevant acidic amino acids instead of three as in KNTase (Ref. 36) or LinB. In the latter cases, one of these three negatively charged residues acts as a catalytic base. S7