Structural Insights into a Unique <em>Legionella pneumophila</em> Effector LidA Recognizing Both GDP and GTP Bound Rab1 in Their Active State

<div><p>The intracellular pathogen <em>Legionella pneumophila</em> hijacks the endoplasmic reticulum (ER)-derived vesicles to create an organelle designated <em>Legionella</em>-containing vacuole (LCV) required for bacterial replication. Maturation of the LCV involved acquisition of Rab1, which is mediated by the bacterial effector protein SidM/DrrA. SidM/DrrA is a bifunctional enzyme having the activity of both Rab1-specific GDP dissociation inhibitor (GDI) displacement factor (GDF) and guanine nucleotide exchange factor (GEF). LidA, another Rab1-interacting bacterial effector protein, was reported to promote SidM/DrrA-mediated recruitment of Rab1 to the LCV as well. Here we report the crystal structures of LidA complexes with GDP- and GTP-bound Rab1 respectively. Structural comparison revealed that GDP-Rab1 bound by LidA exhibits an active and nearly identical conformation with that of GTP-Rab1, suggesting that LidA can disrupt the switch function of Rab1 and render it persistently active. As with GTP, LidA maintains GDP-Rab1 in the active conformation through interaction with its two conserved switch regions. Consistent with the structural observations, biochemical assays showed that LidA binds to GDP- and GTP-Rab1 equally well with an affinity approximately 7.5 nM. We propose that the tight interaction with Rab1 allows LidA to facilitate SidM/DrrA-catalyzed release of Rab1 from GDIs. Taken together, our results support a unique mechanism by which a bacterial effector protein regulates Rab1 recycling.</p> </div

Measurement of binding affinity between LidA and GTP-bound or GDP-bound Rab1 by ITC.

<p>(A) Raw ITC data. Top panel: twenty injections of GTP-bound Rab1(Q70L) solutions were titrated into LidA(188-580) solution in ITC cell. The area of each injection peak corresponds to the total heat released for that injection. Bottom panel: the binding isotherm for GTP-bound Rab1(Q70L) and LidA(188-580) interaction, the integrated heat is plotted against the stoichiometry of 1∶1, data fitting revealed a binding affinity of 7.5 nM. (B) Top panel: twenty injections of GDP-bound Rab1(S25N) solutions were titrated into LidA(188-580) solution in ITC cell. The area of each injection peak corresponds to the total heat released for that injection. Bottom panel: the binding isotherm for GDP-bound Rab1(S25N) and LidA(188-580) interaction, the integrated heat is plotted against the stoichiometry of 1∶1, data fitting revealed a binding affinity of 7.6 nM. Both titrations were performed in the absence of added Mg²⁺ and GDP/GTP.</p

Measurement of binding affinity between LidA and 9 kinds of Rabs by ITC.

<p>(A–G) Raw ITC data. Top panel: twenty injections of Rab2 (A), Rab4 (B), Rab6 (C), Rab7 (D), Rab9 (E), Rab11 (F), Rab20 (G) solutions were titrated into LidA(188-580) solution in ITC cell. The area of each injection peak corresponds to the total heat released for that injection. Bottom panel: the binding isotherm for these Rabs and LidA(188-580) interaction, the integrated heat is plotted against the stoichiometry of 1∶1, data fitting revealed a binding affinity as shown. (H) Raw ITC data. Top panel: twenty injections of Rab22 (H) solutions were titrated into LidA(FL) solution ITC cell, the experiment conditions was exactly the same as the top one unless the LidA is full-length. The <i>K_D</i> values of these Rabs and LidA are shown.</p

Overall structures of LidA and its complex with GDP-bound Rab1.

<p>(A) Schematic representation of LidA fingers and Rab1 function regions, sequences not included in the crystallized proteins are marked with hatched lines and labeled as truncation. (B) Cartoon representation of the overall structure of LidA(224-559)-Rab1(S25N; 1-176) complex. Rab1(S25N) is shown in gray, LidA is colored by fingers as shown in schematic representation, GDP is depicted in sticks. (C) Cartoon representation of the LidA fingers (left) and schematic representation of LidA terminal long coiled-coil domain (right), wheat color represents coiled-coil region in crystal structure, gray color represents extend α-helix predicted by secondary structure analysis. N, N terminus; C, C terminus.</p

13 kinds of Rab GTPase family members could be recognized by LidA <i>in vitro</i>.

<p>(A) Sequence alignment of fifteen different Rabs. The LidA-interacting residues in Rab1 are depicted by triangles. The two sequences underneath the black dashed lines correspond to the members unbound to LidA. (B) The GST-pull down of LidA(FL) by beads-immobilized 15 kinds of GST-Rab family members, Rab20 was His-tagged for exceptional.</p

Interaction of Rab1-LidA shares similar features with that of Rab4-Rabenosyn-5.

<p>(A) Superimposition of Rab1(S25N)-LidA(224-559) complex with Rab4-Rabenosyn-5 complex (PDB ID code 1Z0K). The superimposition of the similar anti-parallel coiled-coil regions is shown. Rab1(S25N) is in gray and LidA is in yellow orange; Rab4 is in light blue and Rabenosyn-5 is in green. (B and C) Similar interfaces of the two complexes. (B) represents the detailed interactions between Rab1(S25N) and LidA. (C) represents the detailed interactions between Rab4 and Rabenosyn-5. The residues involved in interaction are shown as stick representations and denoted by black labels.</p

Interaction interfaces between LidA and Rab1.

<p>(A) Rab1(S25N) is shown with electrostatic surface potentials. Blue and red represent the positive and negative charge potential, respectively. The extensive interactions between Rab1(S25N) switch regions and LidA index finger (smude), middle finger (wheat) and ring finger (light teal) are shown. This Figure is in the same orientation as the right panel of <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002528#ppat-1002528-g002" target="_blank">Figure 2B</a>. (B) The detailed interactions between Rab1 switch I (magentas), switch II (marine), P-loop (limon) and LidA middle finger and ring finger. (C) The detailed interactions between Rab1 switch II and LidA index finger. The interacting residues of Rab1 and LidA are shown in sticks, residues labels are color-coded as corresponding cartoon chains, respectively. Hydrogen bonds are indicated by black dashed lines. Salt bridge is indicated by red dashed lines.</p