(a) Graphical illustration of identification of novel DUBs from L. pneumophila effector proteins. (b) Predicted DUB domain of four putative Legionella DUBs. (c, e) Time-course di-ubiquitin panel …
(a) Di-ubiquitin species were incubated with putative Legionella DUBs and analyzed by immuno-blotting with ubiquitin antibody. (b) HEK293 cell lysates were treated with purified Legionella DUBs and …
(a) Predicted catalytic residues on LotB and LotC. (b, c) Di-Ub cleavage activity assay with wild-type and catalytic mutants of LotB and LotC. (d, e) Activity-based probes (ABPs) test on LotB and …
(a, b) Propargyl (Prg) – ubiquitin or ubiquitin-like modifiers reactivity test on LotB and LotC. Prg-ABPs are incubated with LotB and LotC for 60 min. (c) Sequence alignment of ubiquitin with NEDD8. …
(a, b) Minimal domain boundaries of catalytically active LotB and LotC. Different constructs were cloned based on the predicted OTU-domains and their activity, and were tested with di-Ub panel. (c, d…
The helical lobe between the catalytic Cys loop and the variable loop is shown as bar. The catalytic Cys is highlighted in red and conserved residues are highlighted in yellow.
(a, b) Molecular docking and simulations of monoubiquitin to LotB and LotC. Shown are representative snapshots of the MD simulations. Catalytic cysteine and key residues for the interaction between …
(a, c) Proteomic analysis of interacting partners of LotB and LotC. Catalytically inactive FLAG-LotB (C29A) and FLAG-LotC (C24A) were transfected and immunoprecipitated. Co-precipitated interacting …
Mass spectrometry data used in Figure 5a and b.
FLAG-tagged LotB or LotC-OTU catalytic core was ectopically expressed in U2OS cells and immune-stained with cellular organelle markers (endoplasmic reticulum: Calnexin, mitochondria: TOMM20, Golgi: …
(a, b) Proteomic analysis of interacting partners of LotB together with SdcA and SidC, respectively. Catalytically inactive FLAG-LotB (C29A) was co-transfected with either SdcA or SidC and …
Mass spectrometry data used in Figure 5—figure supplement 2a, b.
Mass spectrometry data used in Figure 5—figure supplement 2c, d.
(a–c) Schematic of the experiment and subsequent validation using western blot. (d, e) Volcano plot depicting the identified proteins with corresponding fold change and p-values. Comparison was done …
Mass spectrometry data used in Figure 6d.
Mass spectrometry data used in Figure 6e.
Legionella proteins | Target proteins | |||||
---|---|---|---|---|---|---|
Name | Aligned region | Name | Aligned region | Probability (%) | Identities (%) | PDB ID_Chain |
Lpg1621 | 195–274 | Viral OTU (CC hemorrhagic fever virus) | 69–157 | 92.59 | 16 | 3PHU_B |
195–274 | Human OTUD2 | 63–140 | 92.52 | 17 | 4BOQ_A | |
195–279 | Human OTUD3 | 59–142 | 92.40 | 13 | 4BOU_A | |
193–278 | Human OTUD5 | 100–183 | 91.18 | 21 | 3PFY_A | |
192–279 | Viral OTU (Farallon virus) | 88–183 | 91.08 | 16 | 6D × 5_B | |
Lpg2529 | 1–310 | Viral OTU (Erve virus) | 17–157 | 96.24 | 18 | 5JZE_A |
7–310 | Viral OTU (Dera Ghazi Khan orthonairovirus) | 25–156 | 96.15 | 18 | 6D × 2_B | |
20–310 | Human Otubain1 | 50–234 | 96.02 | 13 | 2ZFY_A | |
20–310 | Human Otubain2 | 50–233 | 95.84 | 13 | 4FJV_C | |
7–310 | Viral OTU (Taggert virus) | 23–156 | 95.71 | 13 | 6D × 3_D | |
Lpg2411 | 110–216 | Yeast UCH8 | 152–259 | 37.94 | 11 | 3MHS_A |
183–272 | EntA-im (Enterococcus faecium) | 7–89 | 37.06 | 15 | 2BL8_B | |
33–94 | Uncharacterized protein (Corynebacterium diphtheriae) | 7–72 | 36.65 | 21 | 3KDQ_D | |
120–212 | PG0816 (Porphyromonas gingivalis) | 53–139 | 35.31 | 16 | 2APL_A | |
104–114 | PSII reaction center protein K (Cyanidium caldarium) | 2–12 | 32.96 | 36 | 4YUU_X2 | |
Lpg2907 | 117–384 | AvrA (Salmonella typhimurium) | 59–299 | 100 | 11 | 6BE0_A |
158–398 | PopP2 (Arabidopsis thaliana) | 99–339 | 99.93 | 13 | 5W3X_C | |
115–390 | HopZ1a (Pseudomonas syringae) | 54–342 | 99.88 | 10 | 5KLP_C | |
118–275 | XopD (Xanthomonas campestris) | 1–148 | 95.53 | 11 | 2OIX_A | |
95–276 | Human SENP1 | 2–177 | 95.21 | 16 | 2G4D_A |
Values are obtained from the HHpred server (MPI Bioinformatics Toolkit).
Data collection and refinement statistics table.