8ALK

Structure of the Legionella phosphocholine hydrolase Lem3 in complex with its substrate Rab1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


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 Lem3469Legionella pneumophilaMutation(s): 4 
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-1B175Homo sapiensMutation(s): 1 
Gene Names: RAB1B
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0U4 (Homo sapiens)
Explore Q9H0U4 
Go to UniProtKB:  Q9H0U4
PHAROS:  Q9H0U4
GTEx:  ENSG00000174903 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H0U4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OJU (Subject of Investigation/LOI)
Query on OJU

Download Ideal Coordinates CCD File 
H [auth B]2-[[[5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxyethyl-[3-(2-chloranylethanoylamino)propyl]-dimethyl-azanium
C18 H33 Cl N5 O12 P2
WZACJIDOHFHVTD-UHFFFAOYSA-O
GDP
Query on GDP

Download Ideal Coordinates CCD File 
F [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
G [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.332α = 90
b = 119.332β = 90
c = 79.058γ = 120
Software Package:
Software NamePurpose
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

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: 2024-02-07
    Changes: Data collection, Refinement description