8ANP

Legionella effector Lem3 mutant D190A in complex with Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Dephosphocholination by Legionella effector Lem3 functions through remodelling of the switch II region of Rab1b.

Kaspers, M.S.Pogenberg, V.Pett, C.Ernst, S.Ecker, F.Ochtrop, P.Groll, M.Hedberg, C.Itzen, A.

(2023) Nat Commun 14: 2245-2245

  • DOI: https://doi.org/10.1038/s41467-023-37621-7
  • Primary Citation of Related Structures:  
    8AGG, 8ALK, 8ANP

  • PubMed Abstract: 

    Bacterial pathogens often make use of post-translational modifications to manipulate host cells. Legionella pneumophila, the causative agent of Legionnaires disease, secretes the enzyme AnkX that uses cytidine diphosphate-choline to post-translationally modify the human small G-Protein Rab1 with a phosphocholine moiety at Ser76. Later in the infection, the Legionella enzyme Lem3 acts as a dephosphocholinase, hydrolytically removing the phosphocholine. While the molecular mechanism for Rab1 phosphocholination by AnkX has recently been resolved, structural insights into the activity of Lem3 remained elusive. Here, we stabilise the transient Lem3:Rab1b complex by substrate mediated covalent capture. Through crystal structures of Lem3 in the apo form and in complex with Rab1b, we reveal Lem3's catalytic mechanism, showing that it acts on Rab1 by locally unfolding it. Since Lem3 shares high structural similarity with metal-dependent protein phosphatases, our Lem3:Rab1b complex structure also sheds light on how these phosphatases recognise protein substrates.


  • Organizational Affiliation

    Institute of Biochemistry and Signal Transduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistr. 52, 20246, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphocholine hydrolase Lem3
A, B, C, D
468Legionella pneumophilaMutation(s): 1 
Gene Names: lem3lpg0696
EC: 3.1.3
UniProt
Find proteins for Q5ZXN5 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZXN5 
Go to UniProtKB:  Q5ZXN5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZXN5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
N [auth C]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
I [auth B]
L [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
L [auth C],
M [auth C],
O [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.72α = 90
b = 187.69β = 90
c = 193.03γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB1335

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-05-03
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Refinement description