3SFV

Crystal structure of the GDP-bound Rab1a S25N mutant in complex with the coiled-coil domain of LidA from Legionella pneumophila

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

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

Cheng, W., Yin, K., Lu, D., Li, B., Zhu, D., Chen, Y., Zhang, H., Xu, S., Chai, J., Gu, L.

(2012) Plos Pathog. 8: e1002528-e1002528

  • DOI: 10.1371/journal.ppat.1002528
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The intracellular pathogen Legionella pneumophila hijacks the endoplasmic reticulum (ER)-derived vesicles to create an organelle designated Legionella-containing vacuole (LCV) required for bacterial replication. Maturation of the LCV involved acquisi ...

    The intracellular pathogen Legionella pneumophila hijacks the endoplasmic reticulum (ER)-derived vesicles to create an organelle designated Legionella-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.

    Organizational Affiliation: 

    State Key Laboratory of Microbial Technology, Shandong University, Jinan, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rab-1A
A
181Homo sapiensMutation(s): 1 
Gene Names: RAB1A (RAB1)
Find proteins for P62820 (Homo sapiens)
Go to Gene View: RAB1A
Go to UniProtKB:  P62820
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LidA protein, substrate of the Dot/Icm system
B
344N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 154.314α = 90.00
b = 54.673β = 90.00
c = 61.699γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-18
    Type: Initial release