6SKU

Legionella effector AnkX in complex with human Rab1b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 

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This is version 1.1 of the entry. See complete history


Literature

Legionellaeffector AnkX displaces the switch II region for Rab1b phosphocholination.

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

(2020) Sci Adv 6: eaaz8041-eaaz8041

  • DOI: https://doi.org/10.1126/sciadv.aaz8041
  • Primary Citation of Related Structures:  
    6SKU

  • PubMed Abstract: 

    The causative agent of Legionnaires disease, Legionella pneumophila , translocates the phosphocholine transferase AnkX during infection and thereby posttranslationally modifies the small guanosine triphosphatase (GTPase) Rab1 with a phosphocholine moiety at S76 using cytidine diphosphate (CDP)-choline as a cosubstrate. The molecular basis for Rab1 binding and enzymatic modification have remained elusive because of lack of structural information of the low-affinity complex with AnkX. We combined thiol-reactive CDP-choline derivatives with recombinantly introduced cysteines in the AnkX active site to covalently capture the heterocomplex. The resulting crystal structure revealed that AnkX induces displacement of important regulatory elements of Rab1 by placing a β sheet into a conserved hydrophobic pocket, thereby permitting phosphocholine transfer to the active and inactive states of the GTPase. Together, the combination of chemical biology and structural analysis reveals the enzymatic mechanism of AnkX and the family of filamentation induced by cyclic adenosine monophosphate (FIC) proteins.


  • Organizational Affiliation

    Department 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 transferase AnkX803Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 4 
Gene Names: ankXlegA8lpg0695
EC: 2.7.1
UniProt
Find proteins for Q5ZXN6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZXN6 
Go to UniProtKB:  Q5ZXN6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZXN6
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): 0 
Gene Names: RAB1B
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.35α = 90
b = 68.47β = 98.93
c = 137.37γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermanySFB1035

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description