3TKL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.183 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.191 

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
196Homo sapiensMutation(s): 0 
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
267N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.183 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 128.823α = 90.00
b = 49.709β = 99.27
c = 61.702γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-27
    Type: Initial release